From 59eab9000ade7c283b75e907c94bc39c44343f1e Mon Sep 17 00:00:00 2001
From: gmillot <gael.millot@pasteur.fr>
Date: Wed, 21 Sep 2022 17:25:14 +0200
Subject: [PATCH] v1.6 release: miami plot updated
---
README.md | 9 +-
bin/fisher_lod.py | 49 +++-
.../fisher.tsv | 82 ------
.../reports/trace.txt | 7 -
.../PL_family_WGS_fisher_1663355226/res.vcf | 233 ------------------
.../reports/trace.txt | 7 -
.../fisher.tsv | 10 +
.../PL_family_WGS_fisher_1663772349/miami.png | Bin 0 -> 61465 bytes
.../reports/Log_info.txt | 0
.../reports/Run_info.txt | 6 +-
.../reports/dag.dot | 66 +++--
.../reports/fisher_for_vcf.config | 12 +-
.../reports/fisher_report.txt | 0
.../reports/miami_report.txt | 129 ++++++++++
.../reports/report.html | 57 +----
.../reports/timeline.html | 18 +-
.../reports/trace.txt | 7 +
.../PL_family_WGS_fisher_1663772349/res.vcf | 161 ++++++++++++
.../vcf_csq_subfield_titles.txt | 0
.../vcf_info_field_titles.txt | 0
.../fisher.tsv | 2 +-
.../PL_family_WGS_fisher_1663773618/miami.png | Bin 0 -> 81994 bytes
.../reports/Log_info.txt | 0
.../reports/Run_info.txt | 6 +-
.../reports/dag.dot | 66 +++--
.../reports/fisher_for_vcf.config | 8 +-
.../reports/fisher_report.txt | 0
.../reports/miami_report.txt | 129 ++++++++++
.../reports/report.html | 61 ++---
.../reports/timeline.html | 18 +-
.../reports/trace.txt | 7 +
.../res.vcf | 2 +-
.../vcf_csq_subfield_titles.txt | 0
.../vcf_info_field_titles.txt | 0
fisher_for_vcf.config | 4 +-
fisher_for_vcf.nf | 72 ++++--
36 files changed, 671 insertions(+), 557 deletions(-)
delete mode 100644 example of results/PL_family_WGS_fisher_1663355226/fisher.tsv
delete mode 100644 example of results/PL_family_WGS_fisher_1663355226/reports/trace.txt
delete mode 100644 example of results/PL_family_WGS_fisher_1663355226/res.vcf
delete mode 100644 example of results/PL_family_WGS_fisher_1663355634/reports/trace.txt
create mode 100644 example of results/PL_family_WGS_fisher_1663772349/fisher.tsv
create mode 100644 example of results/PL_family_WGS_fisher_1663772349/miami.png
rename example of results/{PL_family_WGS_fisher_1663355226 => PL_family_WGS_fisher_1663772349}/reports/Log_info.txt (100%)
rename example of results/{PL_family_WGS_fisher_1663355226 => PL_family_WGS_fisher_1663772349}/reports/Run_info.txt (89%)
rename example of results/{PL_family_WGS_fisher_1663355634 => PL_family_WGS_fisher_1663772349}/reports/dag.dot (77%)
rename example of results/{PL_family_WGS_fisher_1663355226 => PL_family_WGS_fisher_1663772349}/reports/fisher_for_vcf.config (85%)
rename example of results/{PL_family_WGS_fisher_1663355226 => PL_family_WGS_fisher_1663772349}/reports/fisher_report.txt (100%)
create mode 100644 example of results/PL_family_WGS_fisher_1663772349/reports/miami_report.txt
rename example of results/{PL_family_WGS_fisher_1663355226 => PL_family_WGS_fisher_1663772349}/reports/report.html (99%)
rename example of results/{PL_family_WGS_fisher_1663355226 => PL_family_WGS_fisher_1663772349}/reports/timeline.html (99%)
create mode 100644 example of results/PL_family_WGS_fisher_1663772349/reports/trace.txt
create mode 100644 example of results/PL_family_WGS_fisher_1663772349/res.vcf
rename example of results/{PL_family_WGS_fisher_1663355226 => PL_family_WGS_fisher_1663772349}/vcf_csq_subfield_titles.txt (100%)
rename example of results/{PL_family_WGS_fisher_1663355226 => PL_family_WGS_fisher_1663772349}/vcf_info_field_titles.txt (100%)
rename example of results/{PL_family_WGS_fisher_1663355634 => PL_family_WGS_fisher_1663773618}/fisher.tsv (99%)
create mode 100644 example of results/PL_family_WGS_fisher_1663773618/miami.png
rename example of results/{PL_family_WGS_fisher_1663355634 => PL_family_WGS_fisher_1663773618}/reports/Log_info.txt (100%)
rename example of results/{PL_family_WGS_fisher_1663355634 => PL_family_WGS_fisher_1663773618}/reports/Run_info.txt (89%)
rename example of results/{PL_family_WGS_fisher_1663355226 => PL_family_WGS_fisher_1663773618}/reports/dag.dot (77%)
rename example of results/{PL_family_WGS_fisher_1663355634 => PL_family_WGS_fisher_1663773618}/reports/fisher_for_vcf.config (92%)
rename example of results/{PL_family_WGS_fisher_1663355634 => PL_family_WGS_fisher_1663773618}/reports/fisher_report.txt (100%)
create mode 100644 example of results/PL_family_WGS_fisher_1663773618/reports/miami_report.txt
rename example of results/{PL_family_WGS_fisher_1663355634 => PL_family_WGS_fisher_1663773618}/reports/report.html (99%)
rename example of results/{PL_family_WGS_fisher_1663355634 => PL_family_WGS_fisher_1663773618}/reports/timeline.html (99%)
create mode 100644 example of results/PL_family_WGS_fisher_1663773618/reports/trace.txt
rename example of results/{PL_family_WGS_fisher_1663355634 => PL_family_WGS_fisher_1663773618}/res.vcf (99%)
rename example of results/{PL_family_WGS_fisher_1663355634 => PL_family_WGS_fisher_1663773618}/vcf_csq_subfield_titles.txt (100%)
rename example of results/{PL_family_WGS_fisher_1663355634 => PL_family_WGS_fisher_1663773618}/vcf_info_field_titles.txt (100%)
diff --git a/README.md b/README.md
index 66079ce..095d201 100644
--- a/README.md
+++ b/README.md
@@ -55,8 +55,8 @@ Return also a res.vcf file made from the red.tsv file, mimicing a VCF file, i.e.
<br />
| File | Description |
| --- | --- |
-| **PL_family_WGS_fisher_1663355226** | obtained using the dataset file Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf as sample_path |
-| **PL_family_WGS_fisher_1663355634** | obtained using the dataset file Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz as sample_path |
+| **PL_family_WGS_fisher_1663772349** | obtained using the dataset file Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf as sample_path |
+| **PL_family_WGS_fisher_1663773618** | obtained using the dataset file Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz as sample_path |
See the OUTPUT section for the description of the folder and files.
@@ -269,6 +269,11 @@ Gitlab developers
<br /><br />
## WHAT'S NEW IN
+
+### v1.6
+
+1) miami plot updated
+
### v1.5
1) fields of the VCF (like AC or subfield of CSQ like SIFT) can be added into the tsv file
diff --git a/bin/fisher_lod.py b/bin/fisher_lod.py
index 8a2deb7..87cb4de 100644
--- a/bin/fisher_lod.py
+++ b/bin/fisher_lod.py
@@ -43,6 +43,7 @@
import csv
import sys
import re
+import os.path
from cyvcf2 import VCF, Writer
import scipy.stats as stats
import pandas as pd
@@ -65,7 +66,7 @@ import warnings # for warnings.catch_warnings()
vcf_path = sys.argv[1] # 1st argument: pedigree file name, 1 ID par ligne, sys.argv takes arguments from the bash line command when running a .py script
-ped = sys.argv[2]
+ped_path = sys.argv[2]
region = sys.argv[3]
vcf_info_field_titles_path = sys.argv[4]
tsv_extra_fields = sys.argv[5]
@@ -80,8 +81,8 @@ fisher_report = sys.argv[7]
# vcf_path="/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz"
# vcf_path="/mnt/c/Users/gael/Documents/Git_projects/08002_bourgeron/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz"
-# ped="/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.pedigree.txt" # functions for slivar
-# ped="/mnt/c/Users/gael/Documents/Git_projects/08002_bourgeron/dataset/Dyslexia.pedigree.txt"
+# ped_path="/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.pedigree.txt" # functions for slivar
+# ped_path="/mnt/c/Users/gael/Documents/Git_projects/08002_bourgeron/dataset/Dyslexia.pedigree.txt"
# region=[‘chr7:0-147000000’, ‘chr10:1000000-2000000’]
@@ -230,8 +231,6 @@ csq_subfield_pos = [26]
for i4 in csq_subfield_name: # for each CSQ_ field wanted (polyphen, SIFT)
locals()[i4] = ['NA']
-############ Problem about columns between df3 and df
-
# f = open("test.txt", "a") ; f.write(str(list(range(0, len(subfield_pos)))))
for i3 in list(range(0, len(subfield_pos))):
# f = open("test.txt", "a") ; f.write(str([[v.CHROM, v.POS, v.REF, ''.join(v.ALT), ';'.join([i4[0]+"="+str(i4[1]) for i4 in v.INFO]), gene[i3], impact[i3], consequence[i3], aff, una, oddsratio, pvalue, -np.log10(pvalue), an, subfield_pos[i3]]]) + '\n\n\n\n' + str(i3) + '\n\n\n\n' + str(subfield_pos) + '\n\n\n\n' + str(impact) + '\n\n\n\n')
@@ -266,6 +265,26 @@ csq_subfield_pos = [26]
# reserved words
# end reserved words
# argument primary checking
+if isinstance(vcf_path, str) is not True:
+ sys.exit("\n\n========\n\nError in fisher_lod.py: the vcf_path must be a single character string: \n"+" ".join(vcf_path)+"\n\n========\n\n")
+
+if isinstance(ped_path, str) is not True:
+ sys.exit("\n\n========\n\nError in fisher_lod.py: the ped_path must be a single character string: \n"+" ".join(ped_path)+"\n\n========\n\n")
+
+if isinstance(region, str) is not True:
+ sys.exit("\n\n========\n\nError in fisher_lod.py: the region must be a single character string: \n"+" ".join(region)+"\n\n========\n\n")
+
+if isinstance(vcf_info_field_titles_path, str) is not True:
+ sys.exit("\n\n========\n\nError in fisher_lod.py: the vcf_info_field_titles_path must be a single character string: \n"+" ".join(vcf_info_field_titles_path)+"\n\n========\n\n")
+
+if isinstance(tsv_extra_fields, str) is not True:
+ sys.exit("\n\n========\n\nError in fisher_lod.py: the tsv_extra_fields must be a single character string: \n"+" ".join(tsv_extra_fields)+"\n\n========\n\n")
+
+if isinstance(vcf_csq_subfield_titles_path, str) is not True:
+ sys.exit("\n\n========\n\nError in fisher_lod.py: the vcf_csq_subfield_titles_path must be a single character string: \n"+" ".join(vcf_csq_subfield_titles_path)+"\n\n========\n\n")
+
+if isinstance(fisher_report, str) is not True:
+ sys.exit("\n\n========\n\nError in fisher_lod.py: the fisher_report must be a single character string: \n"+" ".join(fisher_report)+"\n\n========\n\n")
# end argument primary checking
# second round of checking and data preparation
# management of NA arguments
@@ -279,7 +298,19 @@ random.seed(1)
# warn.count <- 0 # not required
# end warning initiation
# other checkings
+if os.path.exists(vcf_path) is not True:
+ sys.exit("\n\n========\n\nError in fisher_lod.py: the vcf_path file does not exist: \n"+" ".join(vcf_path)+"\n\n========\n\n")
+
+if os.path.exists(ped_path) is not True:
+ sys.exit("\n\n========\n\nError in fisher_lod.py: the ped_path file does not exist: \n"+" ".join(ped_path)+"\n\n========\n\n")
+
+if os.path.exists(vcf_info_field_titles_path) is not True:
+ sys.exit("\n\n========\n\nError in fisher_lod.py: the vcf_info_field_titles_path file does not exist: \n"+" ".join(vcf_info_field_titles_path)+"\n\n========\n\n")
+
tsv_extra_fields = tsv_extra_fields.split(' ')
+
+if os.path.exists(vcf_csq_subfield_titles_path) is not True:
+ sys.exit("\n\n========\n\nError in fisher_lod.py: the vcf_csq_subfield_titles_path file does not exist: \n"+" ".join(vcf_csq_subfield_titles_path)+"\n\n========\n\n")
# end other checkings
# reserved word checking
# end reserved word checking
@@ -316,7 +347,7 @@ tsv_extra_fields = tsv_extra_fields.split(' ')
# on crée un dictionnaire qui associe le phenotype a chaque barcode, ici c'est fait un lisant un fichier pedigree
status = dict()
-with open(ped, 'r') as pin:
+with open(ped_path, 'r') as pin:
pin = csv.reader(pin, delimiter='\t')
for row in pin:
status[row[1]]=int(row[5])
@@ -363,7 +394,7 @@ if all([i0 == 'NULL' for i0 in tsv_extra_fields]) is False:
tempo_pos.append(i2)
if all([i1 in vcf_csq_subfield_titles for i1 in csq_subfield_name]) is not True:
- sys.exit("Error in fisher_lod.py: some of the CSQ subfield of the tsv_extra_fields parameter (starting by CSQ_): \n"+" ".join(csq_subfield_name)+"\nare not in the vcf_csq_subfield_titles parameter: \n"+" ".join(vcf_csq_subfield_titles)+"\n")
+ sys.exit("\n\n========\n\nError in fisher_lod.py: some of the CSQ subfield of the tsv_extra_fields parameter (starting by CSQ_): \n"+" ".join(csq_subfield_name)+"\nare not in the vcf_csq_subfield_titles parameter: \n"+" ".join(vcf_csq_subfield_titles)+"\n\n========\n\n")
else:
for i2 in csq_subfield_name:
for i3 in list(range(0, len(vcf_csq_subfield_titles))):
@@ -372,10 +403,10 @@ if all([i0 == 'NULL' for i0 in tsv_extra_fields]) is False:
tsv_extra_fields_wo_csq = [tsv_extra_fields[i1] for i1 in tempo_pos]
if all([i1 in vcf_info_field_titles for i1 in tsv_extra_fields_wo_csq]) is not True:
- sys.exit("Error in fisher_lod.py: not considering CSQ_, some of the tsv_extra_fields parameter values: \n"+" ".join(tsv_extra_fields)+"\nare not in the vcf_info_field_titles parameter: \n"+" ".join(vcf_info_field_titles)+"\n")
+ sys.exit("\n\n========\n\nError in fisher_lod.py: not considering CSQ_, some of the tsv_extra_fields parameter values: \n"+" ".join(tsv_extra_fields)+"\nare not in the vcf_info_field_titles parameter: \n"+" ".join(vcf_info_field_titles)+"\n\n========\n\n")
elif all([i1 in vcf_info_field_titles for i1 in tsv_extra_fields]) is not True:
- sys.exit("Error in fisher_lod.py: some of the tsv_extra_fields parameter values: \n"+" ".join(tsv_extra_fields)+"\nare not in the vcf_info_field_titles parameter: \n"+" ".join(vcf_info_field_titles)+"\n")
+ sys.exit("\n\n========\n\nError in fisher_lod.py: some of the tsv_extra_fields parameter values: \n"+" ".join(tsv_extra_fields)+"\nare not in the vcf_info_field_titles parameter: \n"+" ".join(vcf_info_field_titles)+"\n\n========\n\n")
else:
tsv_extra_fields_wo_csq = tsv_extra_fields
diff --git a/example of results/PL_family_WGS_fisher_1663355226/fisher.tsv b/example of results/PL_family_WGS_fisher_1663355226/fisher.tsv
deleted file mode 100644
index 20cbba9..0000000
--- a/example of results/PL_family_WGS_fisher_1663355226/fisher.tsv
+++ /dev/null
@@ -1,82 +0,0 @@
-CHROM POS REF ALT INFO GENE SEVERITY IMPACT AFF UNAFF OR P_VALUE NEG_LOG10_P_VALUE PATIENT_NB CSQ_TRANSCRIPT_NB SIFT Feature PolyPhen AC AF
-chr1 10146 AC A AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 2, 0: 3, 3: 1} {0: 1, 1: 1} 1.0 1.0 -0.0 8 0 ENST00000423562 7 0.3179999887943268
-chr1 10146 AC A AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 2, 0: 3, 3: 1} {0: 1, 1: 1} 1.0 1.0 -0.0 8 1 ENST00000438504 7 0.3179999887943268
-chr1 10146 AC A AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {1: 2, 0: 3, 3: 1} {0: 1, 1: 1} 1.0 1.0 -0.0 8 2 ENST00000450305 7 0.3179999887943268
-chr1 10146 AC A AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {1: 2, 0: 3, 3: 1} {0: 1, 1: 1} 1.0 1.0 -0.0 8 3 ENST00000456328 7 0.3179999887943268
-chr1 10146 AC A AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 2, 0: 3, 3: 1} {0: 1, 1: 1} 1.0 1.0 -0.0 8 4 ENST00000488147 7 0.3179999887943268
-chr1 10146 AC A AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {1: 2, 0: 3, 3: 1} {0: 1, 1: 1} 1.0 1.0 -0.0 8 5 ENST00000515242 7 0.3179999887943268
-chr1 10146 AC A AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {1: 2, 0: 3, 3: 1} {0: 1, 1: 1} 1.0 1.0 -0.0 8 6 ENST00000518655 7 0.3179999887943268
-chr1 10146 AC A AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 2, 0: 3, 3: 1} {0: 1, 1: 1} 1.0 1.0 -0.0 8 7 ENST00000538476 7 0.3179999887943268
-chr1 10146 AC A AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 2, 0: 3, 3: 1} {0: 1, 1: 1} 1.0 1.0 -0.0 8 8 ENST00000541675 7 0.3179999887943268
-chr1 10177 A C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 1} {} 1.0 -0.0 1 0 ENST00000423562 1 0.0560000017285347
-chr1 10177 A C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 1} {} 1.0 -0.0 1 1 ENST00000438504 1 0.0560000017285347
-chr1 10177 A C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {1: 1} {} 1.0 -0.0 1 2 ENST00000450305 1 0.0560000017285347
-chr1 10177 A C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {1: 1} {} 1.0 -0.0 1 3 ENST00000456328 1 0.0560000017285347
-chr1 10177 A C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 1} {} 1.0 -0.0 1 4 ENST00000488147 1 0.0560000017285347
-chr1 10177 A C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {1: 1} {} 1.0 -0.0 1 5 ENST00000515242 1 0.0560000017285347
-chr1 10177 A C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {1: 1} {} 1.0 -0.0 1 6 ENST00000518655 1 0.0560000017285347
-chr1 10177 A C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 1} {} 1.0 -0.0 1 7 ENST00000538476 1 0.0560000017285347
-chr1 10177 A C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 1} {} 1.0 -0.0 1 8 ENST00000541675 1 0.0560000017285347
-chr1 10255 A AAACCCTAACCCT AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {} {} 1.0 -0.0 0 0 ENST00000423562 2 0.20000000298023224
-chr1 10255 A AAACCCTAACCCT AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {} {} 1.0 -0.0 0 1 ENST00000438504 2 0.20000000298023224
-chr1 10255 A AAACCCTAACCCT AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {} {} 1.0 -0.0 0 2 ENST00000450305 2 0.20000000298023224
-chr1 10255 A AAACCCTAACCCT AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {} {} 1.0 -0.0 0 3 ENST00000456328 2 0.20000000298023224
-chr1 10255 A AAACCCTAACCCT AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {} {} 1.0 -0.0 0 4 ENST00000488147 2 0.20000000298023224
-chr1 10255 A AAACCCTAACCCT AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {} {} 1.0 -0.0 0 5 ENST00000515242 2 0.20000000298023224
-chr1 10255 A AAACCCTAACCCT AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {} {} 1.0 -0.0 0 6 ENST00000518655 2 0.20000000298023224
-chr1 10255 A AAACCCTAACCCT AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {} {} 1.0 -0.0 0 7 ENST00000538476 2 0.20000000298023224
-chr1 10255 A AAACCCTAACCCT AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {} {} 1.0 -0.0 0 8 ENST00000541675 2 0.20000000298023224
-chr1 10335 AACCCTAACCCTAACCCT A AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 1} {} 1.0 -0.0 1 0 ENST00000423562 1 0.0560000017285347
-chr1 10335 AACCCTAACCCTAACCCT A AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 1} {} 1.0 -0.0 1 1 ENST00000438504 1 0.0560000017285347
-chr1 10335 AACCCTAACCCTAACCCT A AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 1} {} 1.0 -0.0 1 2 ENST00000450305 1 0.0560000017285347
-chr1 10335 AACCCTAACCCTAACCCT A AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 1} {} 1.0 -0.0 1 3 ENST00000456328 1 0.0560000017285347
-chr1 10335 AACCCTAACCCTAACCCT A AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 1} {} 1.0 -0.0 1 4 ENST00000488147 1 0.0560000017285347
-chr1 10335 AACCCTAACCCTAACCCT A AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 1} {} 1.0 -0.0 1 5 ENST00000515242 1 0.0560000017285347
-chr1 10335 AACCCTAACCCTAACCCT A AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 1} {} 1.0 -0.0 1 6 ENST00000518655 1 0.0560000017285347
-chr1 10335 AACCCTAACCCTAACCCT A AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 1} {} 1.0 -0.0 1 7 ENST00000538476 1 0.0560000017285347
-chr1 10335 AACCCTAACCCTAACCCT A AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 1} {} 1.0 -0.0 1 8 ENST00000541675 1 0.0560000017285347
-chr1 10337 CCCTAA C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 4} {0: 3} 1.0 -0.0 7 0 ENST00000423562 1 0.0560000017285347
-chr1 10337 CCCTAA C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 4} {0: 3} 1.0 -0.0 7 1 ENST00000438504 1 0.0560000017285347
-chr1 10337 CCCTAA C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 4} {0: 3} 1.0 -0.0 7 2 ENST00000450305 1 0.0560000017285347
-chr1 10337 CCCTAA C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 4} {0: 3} 1.0 -0.0 7 3 ENST00000456328 1 0.0560000017285347
-chr1 10337 CCCTAA C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 4} {0: 3} 1.0 -0.0 7 4 ENST00000488147 1 0.0560000017285347
-chr1 10337 CCCTAA C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 4} {0: 3} 1.0 -0.0 7 5 ENST00000515242 1 0.0560000017285347
-chr1 10337 CCCTAA C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 4} {0: 3} 1.0 -0.0 7 6 ENST00000518655 1 0.0560000017285347
-chr1 10337 CCCTAA C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 4} {0: 3} 1.0 -0.0 7 7 ENST00000538476 1 0.0560000017285347
-chr1 10337 CCCTAA C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 4} {0: 3} 1.0 -0.0 7 8 ENST00000541675 1 0.0560000017285347
-chr1 10354 C A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 1, 0: 1} {} 1.0 -0.0 2 0 ENST00000423562 1 0.04500000178813934
-chr1 10354 C A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 1, 0: 1} {} 1.0 -0.0 2 1 ENST00000438504 1 0.04500000178813934
-chr1 10354 C A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {1: 1, 0: 1} {} 1.0 -0.0 2 2 ENST00000450305 1 0.04500000178813934
-chr1 10354 C A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {1: 1, 0: 1} {} 1.0 -0.0 2 3 ENST00000456328 1 0.04500000178813934
-chr1 10354 C A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 1, 0: 1} {} 1.0 -0.0 2 4 ENST00000488147 1 0.04500000178813934
-chr1 10354 C A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {1: 1, 0: 1} {} 1.0 -0.0 2 5 ENST00000515242 1 0.04500000178813934
-chr1 10354 C A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {1: 1, 0: 1} {} 1.0 -0.0 2 6 ENST00000518655 1 0.04500000178813934
-chr1 10354 C A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 1, 0: 1} {} 1.0 -0.0 2 7 ENST00000538476 1 0.04500000178813934
-chr1 10354 C A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 1, 0: 1} {} 1.0 -0.0 2 8 ENST00000541675 1 0.04500000178813934
-chr1 10387 T C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 1, 1: 1} {} 1.0 -0.0 2 0 ENST00000423562 1 0.04500000178813934
-chr1 10387 T C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 1, 1: 1} {} 1.0 -0.0 2 1 ENST00000438504 1 0.04500000178813934
-chr1 10387 T C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 1, 1: 1} {} 1.0 -0.0 2 2 ENST00000450305 1 0.04500000178813934
-chr1 10387 T C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 1, 1: 1} {} 1.0 -0.0 2 3 ENST00000456328 1 0.04500000178813934
-chr1 10387 T C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 1, 1: 1} {} 1.0 -0.0 2 4 ENST00000488147 1 0.04500000178813934
-chr1 10387 T C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 1, 1: 1} {} 1.0 -0.0 2 5 ENST00000515242 1 0.04500000178813934
-chr1 10387 T C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 1, 1: 1} {} 1.0 -0.0 2 6 ENST00000518655 1 0.04500000178813934
-chr1 10387 T C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 1, 1: 1} {} 1.0 -0.0 2 7 ENST00000538476 1 0.04500000178813934
-chr1 10387 T C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 1, 1: 1} {} 1.0 -0.0 2 8 ENST00000541675 1 0.04500000178813934
-chr1 10390 CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 2, 1: 1} {} 1.0 -0.0 3 0 ENST00000423562 1 0.04500000178813934
-chr1 10390 CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 2, 1: 1} {} 1.0 -0.0 3 1 ENST00000438504 1 0.04500000178813934
-chr1 10390 CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 2, 1: 1} {} 1.0 -0.0 3 2 ENST00000450305 1 0.04500000178813934
-chr1 10390 CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 2, 1: 1} {} 1.0 -0.0 3 3 ENST00000456328 1 0.04500000178813934
-chr1 10390 CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 2, 1: 1} {} 1.0 -0.0 3 4 ENST00000488147 1 0.04500000178813934
-chr1 10390 CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 2, 1: 1} {} 1.0 -0.0 3 5 ENST00000515242 1 0.04500000178813934
-chr1 10390 CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 2, 1: 1} {} 1.0 -0.0 3 6 ENST00000518655 1 0.04500000178813934
-chr1 10390 CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 2, 1: 1} {} 1.0 -0.0 3 7 ENST00000538476 1 0.04500000178813934
-chr1 10390 CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 2, 1: 1} {} 1.0 -0.0 3 8 ENST00000541675 1 0.04500000178813934
-chr1 10403 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 5, 1: 1} {0: 3} inf 1.0 -0.0 9 0 ENST00000423562 1 0.04500000178813934
-chr1 10403 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 5, 1: 1} {0: 3} inf 1.0 -0.0 9 1 ENST00000438504 1 0.04500000178813934
-chr1 10403 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 5, 1: 1} {0: 3} inf 1.0 -0.0 9 2 ENST00000450305 1 0.04500000178813934
-chr1 10403 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 5, 1: 1} {0: 3} inf 1.0 -0.0 9 3 ENST00000456328 1 0.04500000178813934
-chr1 10403 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 5, 1: 1} {0: 3} inf 1.0 -0.0 9 4 ENST00000488147 1 0.04500000178813934
-chr1 10403 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 5, 1: 1} {0: 3} inf 1.0 -0.0 9 5 ENST00000515242 1 0.04500000178813934
-chr1 10403 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| DDX11L1 MODIFIER upstream_gene_variant {0: 5, 1: 1} {0: 3} inf 1.0 -0.0 9 6 ENST00000518655 1 0.04500000178813934
-chr1 10403 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 5, 1: 1} {0: 3} inf 1.0 -0.0 9 7 ENST00000538476 1 0.04500000178813934
-chr1 10403 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 5, 1: 1} {0: 3} inf 1.0 -0.0 9 8 ENST00000541675 1 0.04500000178813934
diff --git a/example of results/PL_family_WGS_fisher_1663355226/reports/trace.txt b/example of results/PL_family_WGS_fisher_1663355226/reports/trace.txt
deleted file mode 100644
index 36aad19..0000000
--- a/example of results/PL_family_WGS_fisher_1663355226/reports/trace.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
-2 15/322193 24332 vcf_subfield_title (1) CACHED 0 2022-09-16 20:26:45.909 3.8s 3.2s 42.9% 104 MB 220.8 MB 13.3 MB 3.1 KB
-1 35/ff0357 31267 WorkflowVersion COMPLETED 0 2022-09-16 21:07:07.764 994ms 336ms 20.0% 3.1 MB 19.2 MB 133.7 KB 1.5 KB
-3 9c/1e3727 31477 Backup COMPLETED 0 2022-09-16 21:07:08.772 606ms 6ms 23.4% 0 0 104.2 KB 342 B
-4 3b/762fdc 31607 fisher (1) COMPLETED 0 2022-09-16 21:07:09.388 4.2s 3.8s 131.9% 149.6 MB 1.4 GB 14.8 MB 167.8 KB
-5 15/680a49 31956 tsv2vcf (1) COMPLETED 0 2022-09-16 21:07:13.741 657ms 54ms 22.0% 3.4 MB 19.2 MB 315.6 KB 171 KB
-6 73/018148 32113 miami_plot (1) FAILED 1 2022-09-16 21:07:14.416 2.8s 2.7s - - - - -
diff --git a/example of results/PL_family_WGS_fisher_1663355226/res.vcf b/example of results/PL_family_WGS_fisher_1663355226/res.vcf
deleted file mode 100644
index 4f7defb..0000000
--- a/example of results/PL_family_WGS_fisher_1663355226/res.vcf
+++ /dev/null
@@ -1,233 +0,0 @@
-##fileformat=VCFv4.2;build by fisher_for_vcf.nf
-##WARNING: This file is not a true VCF since FORMAT AND sample (indiv) columns are not present
-##fileformat=VCFv4.2
-##FILTER=<ID=PASS,Description="All filters passed">
-##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
-##FILTER=<ID=LowQual,Description="Low quality">
-##FILTER=<ID=VQSRTrancheINDEL99.00to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -4.5351 <= x < -0.4741">
-##FILTER=<ID=VQSRTrancheINDEL99.90to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -20794.8907">
-##FILTER=<ID=VQSRTrancheINDEL99.90to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -20794.8907 <= x < -4.5351">
-##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -39178.8364">
-##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -39178.8364 <= x < -2.9039">
-##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
-##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
-##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
-##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
-##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
-##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.7-0-gcfedb67,Date="Tue Aug 04 18:41:02 CEST 2020",Epoch=1596559262546,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[/ccc/work/cont007/fg/fg/biobank/by-soft/varscope/hs37d5/WG_hs37d5_regions.target_split_bed/01.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/dev/shm/hs37d5_all_chr.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/VARIANT_C0011JY/C0011JY_hs37d5_BOTH_01.HC.temp.g.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/VARIANT_C0011JY/C0011JY_hs37d5_BOTH_01.HC.g.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=ApplyVQSR,CommandLine="ApplyVQSR --recal-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-indel-vqsr.recal --tranches-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-indel-vqsr.tranches --output /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-vqsr.vcf.gz --truth-sensitivity-filter-level 99.0 --mode INDEL --variant /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.vcf.gz --reference references/GRCh37/chr/hs37d5.fa --use-allele-specific-annotations false --ignore-all-filters false --exclude-filtered false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.8.1",Date="September 16, 2021 12:50:15 PM CEST">
-##GATKCommandLine=<ID=ApplyVQSR,CommandLine="ApplyVQSR --recal-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.recal --tranches-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.tranches --output /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.vcf.gz --truth-sensitivity-filter-level 99.5 --mode SNP --variant /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-no-vqsr.vcf.gz --reference references/GRCh37/chr/hs37d5.fa --use-allele-specific-annotations false --ignore-all-filters false --exclude-filtered false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.8.1",Date="September 16, 2021 12:31:29 PM CEST">
-##GATKCommandLine=<ID=GenomicsDBImport,CommandLine="GenomicsDBImport --genomicsdb-workspace-path /local/scratch/tmp/38734053_1//Dyslexia.chr1.1-1000000 --overwrite-existing-genomicsdb-workspace true --batch-size 50 --consolidate true --sample-name-map /local/scratch/tmp/38734053_1/sample.map --reader-threads 1 --intervals chr1:1-1000000 --interval-padding 500 --tmp-dir /local/scratch/tmp/38734053_1//tmp/ --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --validate-sample-name-map false --merge-input-intervals false --max-num-intervals-to-import-in-parallel 1 --genomicsdb-shared-posixfs-optimizations false --interval-set-rule UNION --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 0 --cloud-index-prefetch-buffer 0 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.8.1",Date="September 15, 2021 3:11:49 PM CEST">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs --output /local/scratch/tmp/38743216_1/Dyslexia.chr1.1-1000000.genotyped.vcf.gz --only-output-calls-starting-in-intervals true --dbsnp /pasteur/zeus/projets/p02/ghfc_wgs_zeus/tools/ngs-workflow/references/GRCh37/chr/gatk-bundle/dbsnp_138.hg19.vcf.gz --variant gendb:///local/scratch/tmp/38743216_1//Dyslexia.chr1.1-1000000 --intervals chr1:1-1000000 --reference references/GRCh37/chr/hs37d5.fa --annotation-group StandardAnnotation --include-non-variant-sites false --merge-input-intervals false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --keep-combined-raw-annotations false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genomicsdb-use-bcf-codec false --genomicsdb-shared-posixfs-optimizations false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false --allow-old-rms-mapping-quality-annotation-data false",Version="4.1.8.1",Date="September 15, 2021 3:30:43 PM CEST">
-##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --emit-ref-confidence GVCF --standard-min-confidence-threshold-for-calling 10.0 --output /ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/VARIANT_C0011JY/C0011JY_hs37d5_BOTH_01.HC.temp.g.vcf --intervals /ccc/work/cont007/fg/fg/biobank/by-soft/varscope/hs37d5/WG_hs37d5_regions.target_split_bed/01_overlap.bed --input /ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/MAPPING_C0011JY/reliable.realign.recal/A592_DA_C0011JY_H72NKCCX2_hs37d5_MERGE_PE_1_01.reliable.realign.recal.bam --reference /dev/shm/hs37d5_all_chr.fasta --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --adaptive-pruning false --do-not-recover-dangling-branches false --recover-dangling-heads false --consensus false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 1.0 --max-unpruned-variants 100 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --correct-overlapping-quality false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version=4.1.0.0,Date="August 4, 2020 4:14:40 PM CEST">
-##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
-##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
-##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
-##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
-##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
-##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
-##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
-##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
-##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
-##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
-##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants">
-##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants">
-##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
-##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
-##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
-##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
-##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds of being a true variant versus being false under the trained gaussian mixture model">
-##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
-##bcftools_normCommand=norm -m - -w 10000 -f references/GRCh37/chr/hs37d5.fa; Date=Wed Sep 15 15:31:06 2021
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-##contig=<ID=hs37d5,length=35477943>
-##reference=file:///dev/shm/hs37d5_all_chr.fasta
-##source=ApplyVQSR
-##source=GenomicsDBImport
-##source=GenotypeGVCFs
-##source=HaplotypeCaller
-##source=SelectVariants
-##bcftools_normCommand=norm -m - -w 1000 -c s -f references/GRCh37/chr/hs37d5.fa --threads 3 -Oz -o /pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/splitted/Dyslexia.gatk-vqsr.splitted.chr1.1-10000000.norm.vcf.gz; Date=Thu Sep 16 12:54:23 2021
-##VEP="v104" time="2021-09-16 12:54:40" cache="tools/ensembl-vep-104.3/data/homo_sapiens/104_GRCh37" ensembl-variation=104.20f5335 ensembl-funcgen=104.f1c7762 ensembl=104.1af1dce ensembl-io=104.1d3bb6e 1000genomes="phase3" COSMIC="92" ClinVar="202012" HGMD-PUBLIC="20204" assembly="GRCh37.p13" dbSNP="154" gencode="GENCODE 19" genebuild="2011-04" gnomAD="r2.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
-##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|CCDS|SIFT|PolyPhen|HGVS_OFFSET">
-##WARNING: 5 first names of the header of the initial file: CHROM POS REF ALT INFO
-##WARNING: if the 5 first columns of the .tsv file are not CHROM POS REF ALT INFO, then the .vcf file produced by this process is not good
-##INFO=<FISHER=GENE|SEVERITY|IMPACT|AFF|UNAFF|OR|P_VALUE|NEG_LOG10_P_VALUE|PATIENT_NB|CSQ_TRANSCRIPT_NB|SIFT|Feature|PolyPhen|AC|AF>
-#CHROM POS ID REF ALT QUAL FILTER INFO
-chr1 10146 . AC A . . AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 2, 0: 3, 3: 1}|{0: 1, 1: 1}|1.0|1.0|-0.0|8|0||ENST00000423562||7|0.3179999887943268
-chr1 10146 . AC A . . AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 2, 0: 3, 3: 1}|{0: 1, 1: 1}|1.0|1.0|-0.0|8|1||ENST00000438504||7|0.3179999887943268
-chr1 10146 . AC A . . AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{1: 2, 0: 3, 3: 1}|{0: 1, 1: 1}|1.0|1.0|-0.0|8|2||ENST00000450305||7|0.3179999887943268
-chr1 10146 . AC A . . AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{1: 2, 0: 3, 3: 1}|{0: 1, 1: 1}|1.0|1.0|-0.0|8|3||ENST00000456328||7|0.3179999887943268
-chr1 10146 . AC A . . AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 2, 0: 3, 3: 1}|{0: 1, 1: 1}|1.0|1.0|-0.0|8|4||ENST00000488147||7|0.3179999887943268
-chr1 10146 . AC A . . AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{1: 2, 0: 3, 3: 1}|{0: 1, 1: 1}|1.0|1.0|-0.0|8|5||ENST00000515242||7|0.3179999887943268
-chr1 10146 . AC A . . AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{1: 2, 0: 3, 3: 1}|{0: 1, 1: 1}|1.0|1.0|-0.0|8|6||ENST00000518655||7|0.3179999887943268
-chr1 10146 . AC A . . AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 2, 0: 3, 3: 1}|{0: 1, 1: 1}|1.0|1.0|-0.0|8|7||ENST00000538476||7|0.3179999887943268
-chr1 10146 . AC A . . AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 2, 0: 3, 3: 1}|{0: 1, 1: 1}|1.0|1.0|-0.0|8|8||ENST00000541675||7|0.3179999887943268
-chr1 10177 . A C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 1}|{}||1.0|-0.0|1|0||ENST00000423562||1|0.0560000017285347
-chr1 10177 . A C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 1}|{}||1.0|-0.0|1|1||ENST00000438504||1|0.0560000017285347
-chr1 10177 . A C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{1: 1}|{}||1.0|-0.0|1|2||ENST00000450305||1|0.0560000017285347
-chr1 10177 . A C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{1: 1}|{}||1.0|-0.0|1|3||ENST00000456328||1|0.0560000017285347
-chr1 10177 . A C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 1}|{}||1.0|-0.0|1|4||ENST00000488147||1|0.0560000017285347
-chr1 10177 . A C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{1: 1}|{}||1.0|-0.0|1|5||ENST00000515242||1|0.0560000017285347
-chr1 10177 . A C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{1: 1}|{}||1.0|-0.0|1|6||ENST00000518655||1|0.0560000017285347
-chr1 10177 . A C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 1}|{}||1.0|-0.0|1|7||ENST00000538476||1|0.0560000017285347
-chr1 10177 . A C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 1}|{}||1.0|-0.0|1|8||ENST00000541675||1|0.0560000017285347
-chr1 10255 . A AAACCCTAACCCT . . AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{}|{}||1.0|-0.0|0|0||ENST00000423562||2|0.20000000298023224
-chr1 10255 . A AAACCCTAACCCT . . AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{}|{}||1.0|-0.0|0|1||ENST00000438504||2|0.20000000298023224
-chr1 10255 . A AAACCCTAACCCT . . AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{}|{}||1.0|-0.0|0|2||ENST00000450305||2|0.20000000298023224
-chr1 10255 . A AAACCCTAACCCT . . AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{}|{}||1.0|-0.0|0|3||ENST00000456328||2|0.20000000298023224
-chr1 10255 . A AAACCCTAACCCT . . AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{}|{}||1.0|-0.0|0|4||ENST00000488147||2|0.20000000298023224
-chr1 10255 . A AAACCCTAACCCT . . AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{}|{}||1.0|-0.0|0|5||ENST00000515242||2|0.20000000298023224
-chr1 10255 . A AAACCCTAACCCT . . AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{}|{}||1.0|-0.0|0|6||ENST00000518655||2|0.20000000298023224
-chr1 10255 . A AAACCCTAACCCT . . AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{}|{}||1.0|-0.0|0|7||ENST00000538476||2|0.20000000298023224
-chr1 10255 . A AAACCCTAACCCT . . AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{}|{}||1.0|-0.0|0|8||ENST00000541675||2|0.20000000298023224
-chr1 10335 . AACCCTAACCCTAACCCT A . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 1}|{}||1.0|-0.0|1|0||ENST00000423562||1|0.0560000017285347
-chr1 10335 . AACCCTAACCCTAACCCT A . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 1}|{}||1.0|-0.0|1|1||ENST00000438504||1|0.0560000017285347
-chr1 10335 . AACCCTAACCCTAACCCT A . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 1}|{}||1.0|-0.0|1|2||ENST00000450305||1|0.0560000017285347
-chr1 10335 . AACCCTAACCCTAACCCT A . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 1}|{}||1.0|-0.0|1|3||ENST00000456328||1|0.0560000017285347
-chr1 10335 . AACCCTAACCCTAACCCT A . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 1}|{}||1.0|-0.0|1|4||ENST00000488147||1|0.0560000017285347
-chr1 10335 . AACCCTAACCCTAACCCT A . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 1}|{}||1.0|-0.0|1|5||ENST00000515242||1|0.0560000017285347
-chr1 10335 . AACCCTAACCCTAACCCT A . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 1}|{}||1.0|-0.0|1|6||ENST00000518655||1|0.0560000017285347
-chr1 10335 . AACCCTAACCCTAACCCT A . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 1}|{}||1.0|-0.0|1|7||ENST00000538476||1|0.0560000017285347
-chr1 10335 . AACCCTAACCCTAACCCT A . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 1}|{}||1.0|-0.0|1|8||ENST00000541675||1|0.0560000017285347
-chr1 10337 . CCCTAA C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 4}|{0: 3}||1.0|-0.0|7|0||ENST00000423562||1|0.0560000017285347
-chr1 10337 . CCCTAA C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 4}|{0: 3}||1.0|-0.0|7|1||ENST00000438504||1|0.0560000017285347
-chr1 10337 . CCCTAA C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 4}|{0: 3}||1.0|-0.0|7|2||ENST00000450305||1|0.0560000017285347
-chr1 10337 . CCCTAA C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 4}|{0: 3}||1.0|-0.0|7|3||ENST00000456328||1|0.0560000017285347
-chr1 10337 . CCCTAA C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 4}|{0: 3}||1.0|-0.0|7|4||ENST00000488147||1|0.0560000017285347
-chr1 10337 . CCCTAA C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 4}|{0: 3}||1.0|-0.0|7|5||ENST00000515242||1|0.0560000017285347
-chr1 10337 . CCCTAA C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 4}|{0: 3}||1.0|-0.0|7|6||ENST00000518655||1|0.0560000017285347
-chr1 10337 . CCCTAA C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 4}|{0: 3}||1.0|-0.0|7|7||ENST00000538476||1|0.0560000017285347
-chr1 10337 . CCCTAA C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 4}|{0: 3}||1.0|-0.0|7|8||ENST00000541675||1|0.0560000017285347
-chr1 10354 . C A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 1, 0: 1}|{}||1.0|-0.0|2|0||ENST00000423562||1|0.04500000178813934
-chr1 10354 . C A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 1, 0: 1}|{}||1.0|-0.0|2|1||ENST00000438504||1|0.04500000178813934
-chr1 10354 . C A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{1: 1, 0: 1}|{}||1.0|-0.0|2|2||ENST00000450305||1|0.04500000178813934
-chr1 10354 . C A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{1: 1, 0: 1}|{}||1.0|-0.0|2|3||ENST00000456328||1|0.04500000178813934
-chr1 10354 . C A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 1, 0: 1}|{}||1.0|-0.0|2|4||ENST00000488147||1|0.04500000178813934
-chr1 10354 . C A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{1: 1, 0: 1}|{}||1.0|-0.0|2|5||ENST00000515242||1|0.04500000178813934
-chr1 10354 . C A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{1: 1, 0: 1}|{}||1.0|-0.0|2|6||ENST00000518655||1|0.04500000178813934
-chr1 10354 . C A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 1, 0: 1}|{}||1.0|-0.0|2|7||ENST00000538476||1|0.04500000178813934
-chr1 10354 . C A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 1, 0: 1}|{}||1.0|-0.0|2|8||ENST00000541675||1|0.04500000178813934
-chr1 10387 . T C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 1, 1: 1}|{}||1.0|-0.0|2|0||ENST00000423562||1|0.04500000178813934
-chr1 10387 . T C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 1, 1: 1}|{}||1.0|-0.0|2|1||ENST00000438504||1|0.04500000178813934
-chr1 10387 . T C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 1, 1: 1}|{}||1.0|-0.0|2|2||ENST00000450305||1|0.04500000178813934
-chr1 10387 . T C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 1, 1: 1}|{}||1.0|-0.0|2|3||ENST00000456328||1|0.04500000178813934
-chr1 10387 . T C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 1, 1: 1}|{}||1.0|-0.0|2|4||ENST00000488147||1|0.04500000178813934
-chr1 10387 . T C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 1, 1: 1}|{}||1.0|-0.0|2|5||ENST00000515242||1|0.04500000178813934
-chr1 10387 . T C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 1, 1: 1}|{}||1.0|-0.0|2|6||ENST00000518655||1|0.04500000178813934
-chr1 10387 . T C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 1, 1: 1}|{}||1.0|-0.0|2|7||ENST00000538476||1|0.04500000178813934
-chr1 10387 . T C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 1, 1: 1}|{}||1.0|-0.0|2|8||ENST00000541675||1|0.04500000178813934
-chr1 10390 . CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 2, 1: 1}|{}||1.0|-0.0|3|0||ENST00000423562||1|0.04500000178813934
-chr1 10390 . CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 2, 1: 1}|{}||1.0|-0.0|3|1||ENST00000438504||1|0.04500000178813934
-chr1 10390 . CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 2, 1: 1}|{}||1.0|-0.0|3|2||ENST00000450305||1|0.04500000178813934
-chr1 10390 . CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 2, 1: 1}|{}||1.0|-0.0|3|3||ENST00000456328||1|0.04500000178813934
-chr1 10390 . CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 2, 1: 1}|{}||1.0|-0.0|3|4||ENST00000488147||1|0.04500000178813934
-chr1 10390 . CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 2, 1: 1}|{}||1.0|-0.0|3|5||ENST00000515242||1|0.04500000178813934
-chr1 10390 . CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 2, 1: 1}|{}||1.0|-0.0|3|6||ENST00000518655||1|0.04500000178813934
-chr1 10390 . CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 2, 1: 1}|{}||1.0|-0.0|3|7||ENST00000538476||1|0.04500000178813934
-chr1 10390 . CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 2, 1: 1}|{}||1.0|-0.0|3|8||ENST00000541675||1|0.04500000178813934
-chr1 10403 . ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 5, 1: 1}|{0: 3}|inf|1.0|-0.0|9|0||ENST00000423562||1|0.04500000178813934
-chr1 10403 . ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 5, 1: 1}|{0: 3}|inf|1.0|-0.0|9|1||ENST00000438504||1|0.04500000178813934
-chr1 10403 . ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 5, 1: 1}|{0: 3}|inf|1.0|-0.0|9|2||ENST00000450305||1|0.04500000178813934
-chr1 10403 . ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 5, 1: 1}|{0: 3}|inf|1.0|-0.0|9|3||ENST00000456328||1|0.04500000178813934
-chr1 10403 . ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 5, 1: 1}|{0: 3}|inf|1.0|-0.0|9|4||ENST00000488147||1|0.04500000178813934
-chr1 10403 . ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 5, 1: 1}|{0: 3}|inf|1.0|-0.0|9|5||ENST00000515242||1|0.04500000178813934
-chr1 10403 . ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||;FISHER=DDX11L1|MODIFIER|upstream_gene_variant|{0: 5, 1: 1}|{0: 3}|inf|1.0|-0.0|9|6||ENST00000518655||1|0.04500000178813934
-chr1 10403 . ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 5, 1: 1}|{0: 3}|inf|1.0|-0.0|9|7||ENST00000538476||1|0.04500000178813934
-chr1 10403 . ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 5, 1: 1}|{0: 3}|inf|1.0|-0.0|9|8||ENST00000541675||1|0.04500000178813934
diff --git a/example of results/PL_family_WGS_fisher_1663355634/reports/trace.txt b/example of results/PL_family_WGS_fisher_1663355634/reports/trace.txt
deleted file mode 100644
index b88f01d..0000000
--- a/example of results/PL_family_WGS_fisher_1663355634/reports/trace.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
-2 8c/70ebc8 22603 vcf_subfield_title (1) CACHED 0 2022-09-16 20:25:38.989 3.4s 2.8s 46.0% 103 MB 220.1 MB 12.1 MB 3.1 KB
-1 36/992bb0 4312 WorkflowVersion COMPLETED 0 2022-09-16 21:13:56.542 1s 365ms 18.6% 3.2 MB 19.2 MB 133.8 KB 1.5 KB
-3 e1/71e067 4524 Backup COMPLETED 0 2022-09-16 21:13:57.612 616ms 7ms 21.8% 0 0 104.2 KB 342 B
-4 c1/38d1e9 4653 fisher (1) COMPLETED 0 2022-09-16 21:13:58.238 2m 3s 2m 2s 55.8% 183.3 MB 1.4 GB 16.6 MB 13.1 MB
-6 6b/7e6ceb 6575 tsv2vcf (1) COMPLETED 0 2022-09-16 21:16:01.338 3s 2.4s 26.1% 6.6 MB 42.2 MB 13.3 MB 13.3 MB
-5 e7/19507a 6868 miami_plot (1) FAILED 1 2022-09-16 21:16:04.347 3.4s 3.3s - - - - -
diff --git a/example of results/PL_family_WGS_fisher_1663772349/fisher.tsv b/example of results/PL_family_WGS_fisher_1663772349/fisher.tsv
new file mode 100644
index 0000000..a872920
--- /dev/null
+++ b/example of results/PL_family_WGS_fisher_1663772349/fisher.tsv
@@ -0,0 +1,10 @@
+CHROM POS REF ALT INFO GENE IMPACT CONSEQUENCE AFF UNAFF OR P_VALUE NEG_LOG10_P_VALUE PATIENT_NB CSQ_TRANSCRIPT_NB SIFT PolyPhen AC AF
+chr1 10146 AC A AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 2, 0: 3, 3: 1} {0: 1, 1: 1} 1.0 1.0 -0.0 8 NA NA NA 7 0.3179999887943268
+chr1 10177 A C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 1} {} 1.0 -0.0 1 NA NA NA 1 0.0560000017285347
+chr1 10255 A AAACCCTAACCCT AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {} {} 1.0 -0.0 0 NA NA NA 2 0.20000000298023224
+chr1 10335 AACCCTAACCCTAACCCT A AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 1} {} 1.0 -0.0 1 NA NA NA 1 0.0560000017285347
+chr1 10337 CCCTAA C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {0: 4} {0: 3} 1.0 -0.0 7 NA NA NA 1 0.0560000017285347
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diff --git a/example of results/PL_family_WGS_fisher_1663772349/miami.png b/example of results/PL_family_WGS_fisher_1663772349/miami.png
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diff --git a/example of results/PL_family_WGS_fisher_1663355226/reports/Log_info.txt b/example of results/PL_family_WGS_fisher_1663772349/reports/Log_info.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1663355226/reports/Log_info.txt
rename to example of results/PL_family_WGS_fisher_1663772349/reports/Log_info.txt
diff --git a/example of results/PL_family_WGS_fisher_1663355226/reports/Run_info.txt b/example of results/PL_family_WGS_fisher_1663772349/reports/Run_info.txt
similarity index 89%
rename from example of results/PL_family_WGS_fisher_1663355226/reports/Run_info.txt
rename to example of results/PL_family_WGS_fisher_1663772349/reports/Run_info.txt
index 49dcdb3..aca5ac6 100644
--- a/example of results/PL_family_WGS_fisher_1663355226/reports/Run_info.txt
+++ b/example of results/PL_family_WGS_fisher_1663772349/reports/Run_info.txt
@@ -1,9 +1,9 @@
Project (empty means no .git folder where the main.nf file is present): origin git@gitlab.pasteur.fr:gmillot/fisher_for_vcf.git (fetch)
-Git info (empty means no .git folder where the main.nf file is present): 1.3-5-g2d3439c2ba-dirty
+Git info (empty means no .git folder where the main.nf file is present): v1.5-19-g5fa0e4463f-dirty
Cmd line: nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config -resume
execution mode: local
Manifest's pipeline version: null
-result path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1663355226
+result path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1663772349
nextflow version: 21.04.2
@@ -16,5 +16,5 @@ workDir (directory where tasks temporary files are created): /mnt/c/Users/Gael/D
USER VARIABLES:
-out_path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1663355226
+out_path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1663772349
sample_path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf
diff --git a/example of results/PL_family_WGS_fisher_1663355634/reports/dag.dot b/example of results/PL_family_WGS_fisher_1663772349/reports/dag.dot
similarity index 77%
rename from example of results/PL_family_WGS_fisher_1663355634/reports/dag.dot
rename to example of results/PL_family_WGS_fisher_1663772349/reports/dag.dot
index d504cdf..2f0e9f0 100644
--- a/example of results/PL_family_WGS_fisher_1663355634/reports/dag.dot
+++ b/example of results/PL_family_WGS_fisher_1663772349/reports/dag.dot
@@ -4,17 +4,17 @@ p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
p0 -> p1;
p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p25 [label="tsv2vcf"];
-p1 -> p25 [label="vcf_ch3"];
-
-p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p9 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="combine"];
-p1 -> p9 [label="vcf_ch2"];
+p24 [label="tsv2vcf"];
+p1 -> p24 [label="vcf_ch3"];
p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
p8 [label="vcf_subfield_title"];
p1 -> p8 [label="vcf_ch1"];
+p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
+p9 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="combine"];
+p1 -> p9 [label="vcf_ch2"];
+
p2 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.fromPath"];
p11 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="first"];
p2 -> p11 [label="tbi_ch"];
@@ -24,8 +24,8 @@ p10 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="first"];
p3 -> p10 [label="ped_ch"];
p4 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.fromPath"];
-p24 [label="miami_plot"];
-p4 -> p24 [label="chr_ch"];
+p23 [label="miami_plot"];
+p4 -> p23 [label="chr_ch"];
p5 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.from"];
p9 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="combine"];
@@ -68,51 +68,47 @@ p15 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
p14 -> p15;
p15 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p16 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="subscribe"];
-p15 -> p16 [label="fisher_ch2"];
+p23 [label="miami_plot"];
+p15 -> p23 [label="fisher_ch3"];
p15 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p25 [label="tsv2vcf"];
-p15 -> p25 [label="fisher_ch4"];
+p24 [label="tsv2vcf"];
+p15 -> p24 [label="fisher_ch4"];
p15 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p24 [label="miami_plot"];
-p15 -> p24 [label="fisher_ch3"];
+p16 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="subscribe"];
+p15 -> p16 [label="fisher_ch2"];
p17 [shape=point,label="",fixedsize=true,width=0.1];
-p24 [label="miami_plot"];
-p17 -> p24 [label="region_val"];
+p23 [label="miami_plot"];
+p17 -> p23 [label="x_lim_val"];
p18 [shape=point,label="",fixedsize=true,width=0.1];
-p24 [label="miami_plot"];
-p18 -> p24 [label="x_lim"];
+p23 [label="miami_plot"];
+p18 -> p23 [label="bottom_y_column"];
p19 [shape=point,label="",fixedsize=true,width=0.1];
-p24 [label="miami_plot"];
-p19 -> p24 [label="bottom_y_column"];
+p23 [label="miami_plot"];
+p19 -> p23 [label="color_column"];
p20 [shape=point,label="",fixedsize=true,width=0.1];
-p24 [label="miami_plot"];
-p20 -> p24 [label="color_column"];
+p23 [label="miami_plot"];
+p20 -> p23 [label="y_lim1"];
p21 [shape=point,label="",fixedsize=true,width=0.1];
-p24 [label="miami_plot"];
-p21 -> p24 [label="y_lim1"];
+p23 [label="miami_plot"];
+p21 -> p23 [label="y_lim2"];
p22 [shape=point,label="",fixedsize=true,width=0.1];
-p24 [label="miami_plot"];
-p22 -> p24 [label="y_lim2"];
+p23 [label="miami_plot"];
+p22 -> p23 [label="cute_file"];
-p23 [shape=point,label="",fixedsize=true,width=0.1];
-p24 [label="miami_plot"];
-p23 -> p24 [label="cute_file"];
+p25 [shape=point,label="",fixedsize=true,width=0.1];
+p27 [label="Backup"];
+p25 -> p27 [label="config_file"];
p26 [shape=point,label="",fixedsize=true,width=0.1];
-p28 [label="Backup"];
-p26 -> p28 [label="config_file"];
-
-p27 [shape=point,label="",fixedsize=true,width=0.1];
-p28 [label="Backup"];
-p27 -> p28 [label="log_file"];
+p27 [label="Backup"];
+p26 -> p27 [label="log_file"];
}
diff --git a/example of results/PL_family_WGS_fisher_1663355226/reports/fisher_for_vcf.config b/example of results/PL_family_WGS_fisher_1663772349/reports/fisher_for_vcf.config
similarity index 85%
rename from example of results/PL_family_WGS_fisher_1663355226/reports/fisher_for_vcf.config
rename to example of results/PL_family_WGS_fisher_1663772349/reports/fisher_for_vcf.config
index 8c32867..16e4665 100644
--- a/example of results/PL_family_WGS_fisher_1663355226/reports/fisher_for_vcf.config
+++ b/example of results/PL_family_WGS_fisher_1663772349/reports/fisher_for_vcf.config
@@ -22,12 +22,12 @@ env {
chr_path = "/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/hg19_grch37p5_chr_size_cumul.txt" // human chromo infos
//chr_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/reference_genomes/human hg19_grch37/hg19_grch37p5_chr_size_cumul.txt" // human chromo infos
region = "none" // region to parse. Write "chr7:0-147000000, chr10:1000000-2000000" for a single region, "chr7:0-147000000, chr10:1000000-2000000" if two regions, ""chr7" for a whole chromosome, "chr7, chr1" for two chromosomes and "none" for the complete genome // Warning : replace eval() by ast.literal_eval() from ast package in the main py code ?
- tsv_extra_fields = "AC AF CSQ_SIFT CSQ_Feature CSQ_PolyPhen" // subfields from INFO to add as columns in the tsv file. Example: tsv_extra_fields = "AC AF". Write "CSQ_PolyPhen" for a sub field of the CSQ field of INFO. Write "NULL" if not required
- x_lim = "region" // x-axis limits. Either "whole" for the whole genome, or "region" to have the x-axis limited to the region parameter. Not considered if region = "none"
- bottom_y_column = "NULL" // any of the OR, P_VALUE, NEG_LOG10_P_VALUE or PATIENT_NB column of the res.tsv file for the y-axis of the bottom manhattan plot -> miami plot. Can also be an added column through the tsv_extra_fields parameter. Indicated column of field must be quantitative. Write "NULL" to get the res.tsv file and explore the columns before rerunning the nextflow process using - resume. "NULL" generates a simple manhattan plot
- color_column = "NULL" // as for bottom_y_column in order color the dots. Write "NULL" if not required (dots will be alternatively grey and blue, according to chromo order)
- y_lim1 = 5 // max y-axis limit of the top panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Write "NULL" for no particular limit
- y_lim2 = 20 // max y-axis limit of the bottom panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Not considered if bottom_y_column = "NULL"
+ tsv_extra_fields = "AC AF CSQ_SIFT CSQ_PolyPhen" // subfields from INFO to add as columns in the tsv file. Example: tsv_extra_fields = "AC AF". Write "CSQ_PolyPhen" for a sub field of the CSQ field of INFO. Write "NULL" if not required
+ x_lim = "chr1:10000-108000" // x-axis limits. Either "whole" for the whole genome, "region" to have the regions of the region parameter (i.e., "whole" if region == "none"), or a character string written like the region parameter, to have the x-axis limited to the x_lim parameter. Write "NULL" to does not plot results
+ bottom_y_column = "AF" // any of the OR, P_VALUE, NEG_LOG10_P_VALUE or PATIENT_NB column of the res.tsv file for the y-axis of the bottom manhattan plot -> miami plot. Can also be an added column through the tsv_extra_fields parameter. Indicated column of field must be quantitative. Write "NULL" to get the res.tsv file and explore the columns before rerunning the nextflow process using - resume. "NULL" generates a simple manhattan plot
+ color_column = "AF" // as for bottom_y_column in order color the dots. Write "NULL" if not required (dots will be alternatively grey and blue, according to chromo order)
+ y_lim1 = 3 // max y-axis limit of the top panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Write "NULL" for no particular limit
+ y_lim2 = 2 // max y-axis limit of the bottom panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Not considered if bottom_y_column = "NULL"
cute_path = "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.4.0/cute_little_R_functions.R" // single character string indicating the file (and absolute pathway) of the required cute_little_R_functions toolbox. With ethernet connection available, this can also be used: "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/raw/v5.1.0/cute_little_R_functions.R" or local "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
}
diff --git a/example of results/PL_family_WGS_fisher_1663355226/reports/fisher_report.txt b/example of results/PL_family_WGS_fisher_1663772349/reports/fisher_report.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1663355226/reports/fisher_report.txt
rename to example of results/PL_family_WGS_fisher_1663772349/reports/fisher_report.txt
diff --git a/example of results/PL_family_WGS_fisher_1663772349/reports/miami_report.txt b/example of results/PL_family_WGS_fisher_1663772349/reports/miami_report.txt
new file mode 100644
index 0000000..df82abb
--- /dev/null
+++ b/example of results/PL_family_WGS_fisher_1663772349/reports/miami_report.txt
@@ -0,0 +1,129 @@
+
+
+################################################################ miami PROCESS
+
+
+
+
+
+
+################################ RUNNING DATE AND STARTING TIME
+
+
+
+
+2022-09-21 14:59:20
+
+
+
+
+
+
+################################ RUNNING
+
+
+
+
+
+
+################################ RUNNING END
+
+
+
+
+END TIME: 2022-09-21 14:59:21
+
+
+
+
+TOTAL TIME LAPSE: 1S
+
+
+
+
+ALL DATA SAVED IN all_objects.RData
+
+
+
+
+################################ RECAPITULATION OF WARNING MESSAGES
+
+
+
+
+NO WARNING MESSAGE TO REPORT
+
+
+
+
+################################ INITIAL SETTINGS OF PARAMETERS
+
+
+
+erase.objects TRUE
+erase.graphs TRUE
+script miami
+run.way SCRIPT
+command /usr/lib/R/bin/exec/R,--no-echo,--no-restore,--file=/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/bin/miami.R,--args,fisher.tsv,hg19_grch37p5_chr_size_cumul.txt,chr1:10000-108000,AF,AF,3,2,cute_little_R_functions.R,miami_report.txt
+whole chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr23, chr24, chr25, chrY, chrX, chrM
+fisher fisher.tsv
+chr.path hg19_grch37p5_chr_size_cumul.txt
+x.lim chr1:10000-108000
+bottom.y.column AF
+color.column AF
+y.lim1 3
+y.lim2 2
+cute cute_little_R_functions.R
+log miami_report.txt
+
+
+
+
+################################ R SYSTEM AND PACKAGES
+
+
+R version 4.1.2 (2021-11-01)
+Platform: x86_64-pc-linux-gnu (64-bit)
+Running under: Ubuntu 20.04.3 LTS
+
+Matrix products: default
+BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
+LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
+
+locale:
+ [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
+ [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
+ [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
+ [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
+ [9] LC_ADDRESS=C LC_TELEPHONE=C
+[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
+
+attached base packages:
+[1] stats graphics grDevices utils datasets methods base
+
+other attached packages:
+[1] ggplot2_3.3.3 lubridate_1.8.0 qqman_0.1.8
+
+loaded via a namespace (and not attached):
+ [1] assertthat_0.2.1 calibrate_1.7.7 cli_3.2.0 colorspace_2.0-3
+ [5] compiler_4.1.2 crayon_1.5.0 DBI_1.1.2 digest_0.6.29
+ [9] dplyr_1.0.8 ellipsis_0.3.2 fansi_1.0.2 farver_2.1.0
+[13] generics_0.1.2 glue_1.6.2 grid_4.1.2 gridExtra_2.3
+[17] gtable_0.3.0 labeling_0.4.2 lifecycle_1.0.1 magrittr_2.0.2
+[21] MASS_7.3-55 munsell_0.5.0 pillar_1.7.0 pkgconfig_2.0.3
+[25] purrr_0.3.4 R6_2.5.1 rlang_1.0.2 scales_1.1.1
+[29] tibble_3.1.6 tidyselect_1.1.2 utf8_1.2.2 vctrs_0.3.8
+[33] withr_2.5.0
+
+
+
+
+
+################################ JOB END
+
+TIME: 2022-09-21 14:59:21
+
+TOTAL TIME LAPSE: 1S
+
+
+
diff --git a/example of results/PL_family_WGS_fisher_1663355226/reports/report.html b/example of results/PL_family_WGS_fisher_1663772349/reports/report.html
similarity index 99%
rename from example of results/PL_family_WGS_fisher_1663355226/reports/report.html
rename to example of results/PL_family_WGS_fisher_1663772349/reports/report.html
index 74ff00d..2607491 100644
--- a/example of results/PL_family_WGS_fisher_1663355226/reports/report.html
+++ b/example of results/PL_family_WGS_fisher_1663772349/reports/report.html
@@ -18,11 +18,11 @@
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
- <meta name="description" content="Nextflow workflow report for run id [furious_payne]">
+ <meta name="description" content="Nextflow workflow report for run id [exotic_montalcini]">
<meta name="author" content="Paolo Di Tommaso, Phil Ewels">
<link rel="icon" type="image/png" href="https://www.nextflow.io/img/favicon.png" />
- <title>[furious_payne] Nextflow Workflow Report</title>
+ <title>[exotic_montalcini] Nextflow Workflow Report</title>
<style type="text/css">
/*!
@@ -137,7 +137,7 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r
<li class="nav-item"><a class="nav-link" href="#tasks">Tasks</a></li>
</ul>
<span class="navbar-text">
- [furious_payne]
+ [exotic_montalcini]
</span>
</div>
</nav>
@@ -146,58 +146,27 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r
<div class="container">
<h1 class="display-3">Nextflow workflow report</h1>
- <h2 class="text-muted mb-4"><samp>[furious_payne]</samp> <em>(resumed run)</em></h2>
+ <h2 class="text-muted mb-4"><samp>[exotic_montalcini]</samp> <em>(resumed run)</em></h2>
- <div class="alert alert-danger mb-4">
- <h4>Workflow execution completed unsuccessfully!</h4>
- <p>The exit status of the task that caused the workflow execution to fail was: <code>1</code>.</p>
- <p>The full error message was:</p>
- <pre>Error executing process > 'miami_plot (1)'
-
-Caused by:
- Process `miami_plot (1)` terminated with an error exit status (1)
-
-Command executed:
-
- #!/bin/bash -ue
- miami.R fisher.tsv hg19_grch37p5_chr_size_cumul.txt "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr23, chr24, chr25, chrY, chrX, chrM" "region" "NULL" "NULL" "5" "20" "cute_little_R_functions.R" "miami_report.txt"
-
-Command exit status:
- 1
-
-Command output:
-
-
- KIND OF RUN (SCRIPT, COPY-PASTE OR SOURCE): SCRIPT
-
-Command error:
- Error in if (any(diff(tempo) < 0)) { :
- missing value where TRUE/FALSE needed
- In addition: Warning message:
- NAs introduced by coercion
- Execution halted
-
-Work dir:
- /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/work/73/0181480cc3866b9e90bb9422f2f5aa
-
-Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`</pre>
+ <div class="alert alert-success mb-4">
+ Workflow execution completed successfully!
</div>
<dl>
<dt>Run times</dt>
<dd>
- <span id="workflow_start">16-Sep-2022 21:07:06</span> - <span id="workflow_complete">16-Sep-2022 21:07:17</span>
- (<span id="completed_fromnow"></span>duration: <strong>10.7s</strong>)
+ <span id="workflow_start">21-Sep-2022 16:59:10</span> - <span id="workflow_complete">21-Sep-2022 16:59:21</span>
+ (<span id="completed_fromnow"></span>duration: <strong>11.1s</strong>)
</dd>
<dl>
<div class="progress" style="height: 1.6rem; margin: 1.2rem auto; border-radius: 0.20rem;">
- <div style="width: 66.67%" class="progress-bar bg-success" data-toggle="tooltip" data-placement="top" title="4 tasks succeeded"><span class="text-truncate"> 4 succeeded </span></div>
+ <div style="width: 83.33%" class="progress-bar bg-success" data-toggle="tooltip" data-placement="top" title="5 tasks succeeded"><span class="text-truncate"> 5 succeeded </span></div>
<div style="width: 16.67%" class="progress-bar bg-secondary" data-toggle="tooltip" data-placement="top" title="1 tasks were cached"><span class="text-truncate"> 1 cached </span></div>
<div style="width: 0.0%" class="progress-bar bg-warning" data-toggle="tooltip" data-placement="top" title="0 tasks reported and error and were ignored"><span class="text-truncate"> 0 ignored </span></div>
- <div style="width: 16.67%" class="progress-bar bg-danger" data-toggle="tooltip" data-placement="top" title="1 tasks failed"><span class="text-truncate"> 1 failed </span></div>
+ <div style="width: 0.0%" class="progress-bar bg-danger" data-toggle="tooltip" data-placement="top" title="0 tasks failed"><span class="text-truncate"> 0 failed </span></div>
</div>
</dl>
@@ -225,11 +194,11 @@ Tip: view the complete command output by changing to the process work dir and en
<dt class="col-sm-3">Script ID</dt>
- <dd class="col-sm-9"><code>6e134d4f75f8aa0cf8d733c9e9c37df5</code></dd>
+ <dd class="col-sm-9"><code>f8aa46e0a332e25923ce89b43f2c6938</code></dd>
<dt class="col-sm-3">Workflow session</dt>
- <dd class="col-sm-9"><code>22359bce-ba4e-42e0-8d98-e97ed57f40f8</code></dd>
+ <dd class="col-sm-9"><code>20070b19-406b-4731-b65a-fb45186895de</code></dd>
@@ -1060,7 +1029,7 @@ $(function() {
// Nextflow report data
window.data = { "trace":[
-{"task_id":"1","hash":"35\/ff0357","native_id":"31267","process":"WorkflowVersion","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"WorkflowVersion","status":"COMPLETED","exit":"0","submit":"1663355227764","start":"1663355227798","complete":"1663355228758","duration":"994","realtime":"336","%cpu":"20.0","%mem":"0.0","rss":"3207168","vmem":"20148224","peak_rss":"3207168","peak_vmem":"20148224","rchar":"136955","wchar":"1541","syscr":"270","syscw":"35","read_bytes":"3318784","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/35\/ff03573c85eadb6e4a46f9328db5c8","script":"\n echo \"Project (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf remote -v | head -n 1) > Run_info.txt # works only if the main script run is located in a directory that has a .git folder, i.e., that is connected to a distant repo\n echo \"Git info (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf describe --abbrev=10 --dirty --always --tags) >> Run_info.txt # idem. Provide the small commit number of the script and nextflow.config used in the execution\n echo \"Cmd line: nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config -resume\" >> Run_info.txt\n echo \"execution mode\": local >> Run_info.txt\n modules= # this is just to deal with variable interpretation during the creation of the .command.sh file by nextflow. See also $modules below\n if [[ ! -z $modules ]] ; then\n echo \"loaded modules (according to specification by the user thanks to the --modules argument of main.nf)\": >> Run_info.txt\n fi\n echo \"Manifest\'s pipeline version: null\" >> Run_info.txt\n echo \"result path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663355226\" >> Run_info.txt\n echo \"nextflow version: 21.04.2\" >> Run_info.txt\n echo -e \"\\n\\nIMPLICIT VARIABLES:\\n\\nlaunchDir (directory where the workflow is run): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nprojectDir (directory where the main.nf script is located): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nworkDir (directory where tasks temporary files are created): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\" >> Run_info.txt\n echo -e \"\\n\\nUSER VARIABLES:\\n\\nout_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663355226\\nsample_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\" >> Run_info.txt\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_Feature CSQ_PolyPhen\nx_lim=region\nbottom_y_column=NULL\ncolor_column=NULL\ny_lim1=5\ny_lim2=20\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663355226\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"10","inv_ctxt":"0"},{"task_id":"2","hash":"15\/322193","native_id":"24332","process":"vcf_subfield_title","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-r_v4.1.2_extended_v2.1-gitlab_v8.8.img","tag":"-","name":"vcf_subfield_title (1)","status":"CACHED","exit":"0","submit":"1663352805909","start":"1663352805989","complete":"1663352809679","duration":"3770","realtime":"3243","%cpu":"42.9","%mem":"0.1","rss":"109047808","vmem":"231460864","peak_rss":"109047808","peak_vmem":"231530496","rchar":"13945964","wchar":"3159","syscr":"2852","syscw":"243","read_bytes":"17006592","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/15\/3221933e0b05e17c2155737d38441f","script":"\n #!\/bin\/bash -ue\n vcf_subfield_title.R Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf \"cute_little_R_functions.R\" \"miami_report.txt\"\n ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen CSQ_Feature\nx_lim=region\nbottom_y_column=NULL\ncolor_column=NULL\ny_lim1=5\ny_lim2=20\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663352801\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"13321","inv_ctxt":"6"},{"task_id":"3","hash":"9c\/1e3727","native_id":"31477","process":"Backup","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"Backup","status":"COMPLETED","exit":"0","submit":"1663355228772","start":"1663355228858","complete":"1663355229378","duration":"606","realtime":"6","%cpu":"23.4","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"106724","wchar":"342","syscr":"189","syscw":"14","read_bytes":"329728","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/9c\/1e3727b98ae400f5f6f2bdd3c5e570","script":"\n echo -e \"full .nextflow.log is in: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nThe one in the result folder is not complete (miss the end)\" > Log_info.txt\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_Feature CSQ_PolyPhen\nx_lim=region\nbottom_y_column=NULL\ncolor_column=NULL\ny_lim1=5\ny_lim2=20\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663355226\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"4","hash":"3b\/762fdc","native_id":"31607","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (1)","status":"COMPLETED","exit":"0","submit":"1663355229388","start":"1663355229477","complete":"1663355233618","duration":"4230","realtime":"3766","%cpu":"131.9","%mem":"0.1","rss":"156868608","vmem":"1481875456","peak_rss":"156868608","peak_vmem":"1481908224","rchar":"15518561","wchar":"171847","syscr":"2116","syscw":"275","read_bytes":"53007360","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/3b\/762fdcdcc4037eaf65b736e6e208fa","script":"\n #!\/bin\/bash -ue\n fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf Dyslexia.pedigree.txt \"chr1\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_Feature CSQ_PolyPhen\" \"vcf_csq_subfield_titles.txt\" \"fisher_report.txt\"\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_Feature CSQ_PolyPhen\nx_lim=region\nbottom_y_column=NULL\ncolor_column=NULL\ny_lim1=5\ny_lim2=20\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663355226\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"7246","inv_ctxt":"15"},{"task_id":"5","hash":"15\/680a49","native_id":"31956","process":"tsv2vcf","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"tsv2vcf (1)","status":"COMPLETED","exit":"0","submit":"1663355233741","start":"1663355233818","complete":"1663355234398","duration":"657","realtime":"54","%cpu":"22.0","%mem":"0.0","rss":"3530752","vmem":"20160512","peak_rss":"3530752","peak_vmem":"20160512","rchar":"323164","wchar":"175064","syscr":"312","syscw":"235","read_bytes":"367616","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/15\/680a49fc47c82af642fc2b9807feb1","script":"\n #!\/bin\/bash -ue\n PREHEADER=\'##fileformat=VCFv4.2;build by fisher_for_vcf.nf\\n##WARNING: This file is not a true VCF since FORMAT AND sample (indiv) columns are not present\'\n HEADER=\'#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\'\n echo -e $PREHEADER > res.vcf\n FILENAME=$(basename -- \"Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\") # recover a file name without path\n FILE_EXTENSION=\"${FILENAME##*.}\" # ## means \"delete the longest regex starting at the beginning of the tested string\". If nothing, delete nothing. Thus ##*. means delete the longest string finishing by a dot. Use # instead of ## for \"delete the shortest regex starting at the beginning of the tested string\"\n if [[ \"${FILE_EXTENSION}\" =~ gz ]] ; then\n zcat Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf | awk \'{\n if($0 ~ \"^##.*\"){\n print $0\n }else{\n exit 0\n }\n }\' >> res.vcf\n else\n awk \'{\n if($0 ~ \"^##.*\"){\n print $0\n }else{\n exit 0\n }\n }\' Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf >> res.vcf\n fi\n awk -v var1=$HEADER \'BEGIN{FS=\"\\t\" ; OFS=\"\" ; ORS=\"\"}\n NR==1{\n print \"##WARNING: 5 first names of the header of the initial file: \"$1\" \"$2\" \"$3\" \"$4\" \"$5\"\\n\" ;\n print \"##WARNING: if the 5 first columns of the .tsv file are not CHROM POS REF ALT INFO, then the .vcf file produced by this process is not good\\n\" ;\n print \"##INFO=<FISHER=\" ;\n for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n print \">\\n\" ;\n print var1\"\\n\"\n }\n NR > 1{\n gsub(\"[\\\\[\\\\]\\\'\"\'\"\']\", \"\", $4)\n print $1\"\\t\"$2\"\\t.\\t\"$3\"\\t\"$4\"\\t.\\t.\\t\"$5\";FISHER=\" ;\n for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n print \"\\n\"\n }\n \' fisher.tsv >> res.vcf\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_Feature CSQ_PolyPhen\nx_lim=region\nbottom_y_column=NULL\ncolor_column=NULL\ny_lim1=5\ny_lim2=20\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663355226\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"32","inv_ctxt":"5"},{"task_id":"6","hash":"73\/018148","native_id":"32113","process":"miami_plot","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-r_v4.1.2_extended_v2.1-gitlab_v8.8.img","tag":"-","name":"miami_plot (1)","status":"FAILED","exit":"1","submit":"1663355234416","start":"1663355234499","complete":"1663355237188","duration":"2772","realtime":"2689","%cpu":"-","%mem":"-","rss":"-","vmem":"-","peak_rss":"-","peak_vmem":"-","rchar":"-","wchar":"-","syscr":"-","syscw":"-","read_bytes":"-","write_bytes":"-","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/73\/0181480cc3866b9e90bb9422f2f5aa","script":"\n #!\/bin\/bash -ue\n miami.R fisher.tsv hg19_grch37p5_chr_size_cumul.txt \"chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr23, chr24, chr25, chrY, chrX, chrM\" \"region\" \"NULL\" \"NULL\" \"5\" \"20\" \"cute_little_R_functions.R\" \"miami_report.txt\"\n ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_Feature CSQ_PolyPhen\nx_lim=region\nbottom_y_column=NULL\ncolor_column=NULL\ny_lim1=5\ny_lim2=20\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663355226\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"TERMINATE","vol_ctxt":"-","inv_ctxt":"-"}], 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(1)","q2Label":"tsv2vcf (1)","q3Label":"tsv2vcf (1)"},"writes":{"mean":175064,"min":175064,"q1":175064,"q2":175064,"q3":175064,"max":175064,"minLabel":"tsv2vcf (1)","maxLabel":"tsv2vcf (1)","q1Label":"tsv2vcf (1)","q2Label":"tsv2vcf (1)","q3Label":"tsv2vcf (1)"}},{"cpuUsage":null,"process":"miami_plot","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":2689,"min":2689,"q1":2689,"q2":2689,"q3":2689,"max":2689,"minLabel":"miami_plot (1)","maxLabel":"miami_plot (1)","q1Label":"miami_plot (1)","q2Label":"miami_plot (1)","q3Label":"miami_plot (1)"},"writes":null}] };
+{"task_id":"1","hash":"e8\/b45589","native_id":"5355","process":"WorkflowVersion","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"WorkflowVersion","status":"COMPLETED","exit":"0","submit":"1663772351824","start":"1663772351862","complete":"1663772352847","duration":"1023","realtime":"398","%cpu":"18.8","%mem":"0.0","rss":"5287936","vmem":"40296448","peak_rss":"5287936","peak_vmem":"40296448","rchar":"136853","wchar":"1535","syscr":"272","syscw":"35","read_bytes":"4039680","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/e8\/b45589716399a316579c2fad87f39d","script":"\n echo \"Project (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf remote -v | head -n 1) > Run_info.txt # works only if the main script run is located in a directory that has a .git folder, i.e., that is connected to a distant repo\n echo \"Git info (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf describe --abbrev=10 --dirty --always --tags) >> Run_info.txt # idem. Provide the small commit number of the script and nextflow.config used in the execution\n echo \"Cmd line: nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config -resume\" >> Run_info.txt\n echo \"execution mode\": local >> Run_info.txt\n modules= # this is just to deal with variable interpretation during the creation of the .command.sh file by nextflow. See also $modules below\n if [[ ! -z $modules ]] ; then\n echo \"loaded modules (according to specification by the user thanks to the --modules argument of main.nf)\": >> Run_info.txt\n fi\n echo \"Manifest\'s pipeline version: null\" >> Run_info.txt\n echo \"result path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663772349\" >> Run_info.txt\n echo \"nextflow version: 21.04.2\" >> Run_info.txt\n echo -e \"\\n\\nIMPLICIT VARIABLES:\\n\\nlaunchDir (directory where the workflow is run): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nprojectDir (directory where the main.nf script is located): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nworkDir (directory where tasks temporary files are created): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\" >> Run_info.txt\n echo -e \"\\n\\nUSER VARIABLES:\\n\\nout_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663772349\\nsample_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\" >> Run_info.txt\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1:10000-108000\nbottom_y_column=AF\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663772349\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"11","inv_ctxt":"0"},{"task_id":"2","hash":"93\/aea81a","native_id":"8193","process":"vcf_subfield_title","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-r_v4.1.2_extended_v2.1-gitlab_v8.8.img","tag":"-","name":"vcf_subfield_title (1)","status":"CACHED","exit":"0","submit":"1663600640850","start":"1663600640942","complete":"1663600644383","duration":"3533","realtime":"3016","%cpu":"40.6","%mem":"0.1","rss":"108113920","vmem":"230436864","peak_rss":"108113920","peak_vmem":"230469632","rchar":"13945820","wchar":"3150","syscr":"2852","syscw":"243","read_bytes":"16828416","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/93\/aea81a83f0da2705d7f5f4b4d398e4","script":"\n #!\/bin\/bash -ue\n vcf_subfield_title.R Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf \"cute_little_R_functions.R\" \"miami_report.txt\"\n ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=region\nbottom_y_column=NULL\ncolor_column=NULL\ny_lim1=5\ny_lim2=20\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663600637\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"9175","inv_ctxt":"7"},{"task_id":"3","hash":"ee\/1aba37","native_id":"5563","process":"Backup","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"Backup","status":"COMPLETED","exit":"0","submit":"1663772352859","start":"1663772352948","complete":"1663772353397","duration":"538","realtime":"6","%cpu":"25.2","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"106579","wchar":"332","syscr":"189","syscw":"14","read_bytes":"329728","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/ee\/1aba370222d32d526a0ba8911562f2","script":"\n echo -e \"full .nextflow.log is in: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nThe one in the result folder is not complete (miss the end)\" > Log_info.txt\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1:10000-108000\nbottom_y_column=AF\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663772349\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"4","hash":"e2\/20ce33","native_id":"5693","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (1)","status":"COMPLETED","exit":"0","submit":"1663772353408","start":"1663772353497","complete":"1663772356928","duration":"3520","realtime":"3049","%cpu":"154.4","%mem":"0.1","rss":"143917056","vmem":"1462308864","peak_rss":"143917056","peak_vmem":"1462341632","rchar":"15526661","wchar":"16742","syscr":"2121","syscw":"15","read_bytes":"53284864","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/e2\/20ce3335780ad313d1ed96aa87e8d3","script":"\n #!\/bin\/bash -ue\n fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf Dyslexia.pedigree.txt \"chr1\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" \"vcf_csq_subfield_titles.txt\" \"fisher_report.txt\"\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1:10000-108000\nbottom_y_column=AF\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663772349\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3383","inv_ctxt":"4"},{"task_id":"5","hash":"3f\/a12c88","native_id":"5987","process":"tsv2vcf","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"tsv2vcf (1)","status":"COMPLETED","exit":"0","submit":"1663772357048","start":"1663772357127","complete":"1663772357647","duration":"599","realtime":"37","%cpu":"16.9","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"190918","wchar":"42018","syscr":"270","syscw":"75","read_bytes":"367616","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/3f\/a12c8814b4ee81060a1e9bb7630d13","script":"\n #!\/bin\/bash -ue\n PREHEADER=\'##fileformat=VCFv4.2;build by fisher_for_vcf.nf\\n##WARNING: This file is not a true VCF since FORMAT AND sample (indiv) columns are not present\'\n HEADER=\'#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\'\n echo -e $PREHEADER > res.vcf\n FILENAME=$(basename -- \"Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\") # recover a file name without path\n FILE_EXTENSION=\"${FILENAME##*.}\" # ## means \"delete the longest regex starting at the beginning of the tested string\". If nothing, delete nothing. Thus ##*. means delete the longest string finishing by a dot. Use # instead of ## for \"delete the shortest regex starting at the beginning of the tested string\"\n if [[ \"${FILE_EXTENSION}\" =~ gz ]] ; then\n zcat Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf | awk \'{\n if($0 ~ \"^##.*\"){\n print $0\n }else{\n exit 0\n }\n }\' >> res.vcf\n else\n awk \'{\n if($0 ~ \"^##.*\"){\n print $0\n }else{\n exit 0\n }\n }\' Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf >> res.vcf\n fi\n awk -v var1=$HEADER \'BEGIN{FS=\"\\t\" ; OFS=\"\" ; ORS=\"\"}\n NR==1{\n print \"##WARNING: 5 first names of the header of the initial file: \"$1\" \"$2\" \"$3\" \"$4\" \"$5\"\\n\" ;\n print \"##WARNING: if the 5 first columns of the .tsv file are not CHROM POS REF ALT INFO, then the .vcf file produced by this process is not good\\n\" ;\n print \"##INFO=<FISHER=\" ;\n for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n print \">\\n\" ;\n print var1\"\\n\"\n }\n NR > 1{\n gsub(\"[\\\\[\\\\]\\\'\"\'\"\']\", \"\", $4)\n print $1\"\\t\"$2\"\\t.\\t\"$3\"\\t\"$4\"\\t.\\t.\\t\"$5\";FISHER=\" ;\n for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n print \"\\n\"\n }\n \' fisher.tsv >> res.vcf\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1:10000-108000\nbottom_y_column=AF\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663772349\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"6","hash":"92\/260f7f","native_id":"6145","process":"miami_plot","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-r_v4.1.2_extended_v2.1-gitlab_v8.8.img","tag":"-","name":"miami_plot (1)","status":"COMPLETED","exit":"0","submit":"1663772357655","start":"1663772357747","complete":"1663772361417","duration":"3762","realtime":"3272","%cpu":"60.2","%mem":"0.1","rss":"136130560","vmem":"277450752","peak_rss":"160698368","peak_vmem":"303407104","rchar":"14920220","wchar":"65078","syscr":"2598","syscw":"221","read_bytes":"42122240","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/92\/260f7fb7ff6bbb6703dc1955c1d0f0","script":"\n #!\/bin\/bash -ue\n miami.R fisher.tsv hg19_grch37p5_chr_size_cumul.txt \"chr1:10000-108000\" \"AF\" \"AF\" \"3\" \"2\" \"cute_little_R_functions.R\" \"miami_report.txt\"\n ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1:10000-108000\nbottom_y_column=AF\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663772349\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3146","inv_ctxt":"5"}], "summary":[{"cpuUsage":{"mean":40.6,"min":40.6,"q1":40.6,"q2":40.6,"q3":40.6,"max":40.6,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title (1)"},"process":"vcf_subfield_title","mem":{"mean":108113920,"min":108113920,"q1":108113920,"q2":108113920,"q3":108113920,"max":108113920,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title (1)"},"memUsage":{"mean":0.16,"min":0.16,"q1":0.16,"q2":0.16,"q3":0.16,"max":0.16,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title (1)"},"timeUsage":null,"vmem":{"mean":230469632,"min":230469632,"q1":230469632,"q2":230469632,"q3":230469632,"max":230469632,"minLabel":"vcf_subfield_title 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diff --git a/example of results/PL_family_WGS_fisher_1663355226/reports/timeline.html b/example of results/PL_family_WGS_fisher_1663772349/reports/timeline.html
similarity index 99%
rename from example of results/PL_family_WGS_fisher_1663355226/reports/timeline.html
rename to example of results/PL_family_WGS_fisher_1663772349/reports/timeline.html
index 297437c..c9b7b69 100644
--- a/example of results/PL_family_WGS_fisher_1663355226/reports/timeline.html
+++ b/example of results/PL_family_WGS_fisher_1663772349/reports/timeline.html
@@ -205,16 +205,16 @@ $(function() {
// Nextflow report data
window.data = {
- "elapsed": "11.1s",
- "beginningMillis": 1663352805909,
- "endingMillis": 1663355237748,
+ "elapsed": "11.5s",
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+ "endingMillis": 1663772361927,
"processes": [
- {"label": "WorkflowVersion", "cached": false, "index": 0, "times": [{"starting_time": 1663355227764, "ending_time": 1663355227798}, {"starting_time": 1663355227798, "ending_time": 1663355228134, "label": "994ms \/ 3.1 MB"}, {"starting_time": 1663355228134, "ending_time": 1663355228758}]},
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diff --git a/example of results/PL_family_WGS_fisher_1663772349/reports/trace.txt b/example of results/PL_family_WGS_fisher_1663772349/reports/trace.txt
new file mode 100644
index 0000000..47abd68
--- /dev/null
+++ b/example of results/PL_family_WGS_fisher_1663772349/reports/trace.txt
@@ -0,0 +1,7 @@
+task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
+2 93/aea81a 8193 vcf_subfield_title (1) CACHED 0 2022-09-19 17:17:20.850 3.5s 3s 40.6% 103.1 MB 219.8 MB 13.3 MB 3.1 KB
+1 e8/b45589 5355 WorkflowVersion COMPLETED 0 2022-09-21 16:59:11.824 1s 398ms 18.8% 5 MB 38.4 MB 133.6 KB 1.5 KB
+3 ee/1aba37 5563 Backup COMPLETED 0 2022-09-21 16:59:12.859 538ms 6ms 25.2% 0 0 104.1 KB 332 B
+4 e2/20ce33 5693 fisher (1) COMPLETED 0 2022-09-21 16:59:13.408 3.5s 3s 154.4% 137.2 MB 1.4 GB 14.8 MB 16.3 KB
+5 3f/a12c88 5987 tsv2vcf (1) COMPLETED 0 2022-09-21 16:59:17.048 599ms 37ms 16.9% 0 0 186.4 KB 41 KB
+6 92/260f7f 6145 miami_plot (1) COMPLETED 0 2022-09-21 16:59:17.655 3.8s 3.3s 60.2% 153.3 MB 289.4 MB 14.2 MB 63.6 KB
diff --git a/example of results/PL_family_WGS_fisher_1663772349/res.vcf b/example of results/PL_family_WGS_fisher_1663772349/res.vcf
new file mode 100644
index 0000000..15d6922
--- /dev/null
+++ b/example of results/PL_family_WGS_fisher_1663772349/res.vcf
@@ -0,0 +1,161 @@
+##fileformat=VCFv4.2;build by fisher_for_vcf.nf
+##WARNING: This file is not a true VCF since FORMAT AND sample (indiv) columns are not present
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=VQSRTrancheINDEL99.00to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -4.5351 <= x < -0.4741">
+##FILTER=<ID=VQSRTrancheINDEL99.90to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -20794.8907">
+##FILTER=<ID=VQSRTrancheINDEL99.90to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -20794.8907 <= x < -4.5351">
+##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -39178.8364">
+##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -39178.8364 <= x < -2.9039">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
+##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.7-0-gcfedb67,Date="Tue Aug 04 18:41:02 CEST 2020",Epoch=1596559262546,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[/ccc/work/cont007/fg/fg/biobank/by-soft/varscope/hs37d5/WG_hs37d5_regions.target_split_bed/01.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/dev/shm/hs37d5_all_chr.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/VARIANT_C0011JY/C0011JY_hs37d5_BOTH_01.HC.temp.g.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/VARIANT_C0011JY/C0011JY_hs37d5_BOTH_01.HC.g.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine=<ID=ApplyVQSR,CommandLine="ApplyVQSR --recal-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-indel-vqsr.recal --tranches-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-indel-vqsr.tranches --output /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-vqsr.vcf.gz --truth-sensitivity-filter-level 99.0 --mode INDEL --variant /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.vcf.gz --reference references/GRCh37/chr/hs37d5.fa --use-allele-specific-annotations false --ignore-all-filters false --exclude-filtered false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.8.1",Date="September 16, 2021 12:50:15 PM CEST">
+##GATKCommandLine=<ID=ApplyVQSR,CommandLine="ApplyVQSR --recal-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.recal --tranches-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.tranches --output /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.vcf.gz --truth-sensitivity-filter-level 99.5 --mode SNP --variant /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-no-vqsr.vcf.gz --reference references/GRCh37/chr/hs37d5.fa --use-allele-specific-annotations false --ignore-all-filters false --exclude-filtered false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.8.1",Date="September 16, 2021 12:31:29 PM CEST">
+##GATKCommandLine=<ID=GenomicsDBImport,CommandLine="GenomicsDBImport --genomicsdb-workspace-path /local/scratch/tmp/38734053_1//Dyslexia.chr1.1-1000000 --overwrite-existing-genomicsdb-workspace true --batch-size 50 --consolidate true --sample-name-map /local/scratch/tmp/38734053_1/sample.map --reader-threads 1 --intervals chr1:1-1000000 --interval-padding 500 --tmp-dir /local/scratch/tmp/38734053_1//tmp/ --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --validate-sample-name-map false --merge-input-intervals false --max-num-intervals-to-import-in-parallel 1 --genomicsdb-shared-posixfs-optimizations false --interval-set-rule UNION --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 0 --cloud-index-prefetch-buffer 0 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.8.1",Date="September 15, 2021 3:11:49 PM CEST">
+##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs --output /local/scratch/tmp/38743216_1/Dyslexia.chr1.1-1000000.genotyped.vcf.gz --only-output-calls-starting-in-intervals true --dbsnp /pasteur/zeus/projets/p02/ghfc_wgs_zeus/tools/ngs-workflow/references/GRCh37/chr/gatk-bundle/dbsnp_138.hg19.vcf.gz --variant gendb:///local/scratch/tmp/38743216_1//Dyslexia.chr1.1-1000000 --intervals chr1:1-1000000 --reference references/GRCh37/chr/hs37d5.fa --annotation-group StandardAnnotation --include-non-variant-sites false --merge-input-intervals false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --keep-combined-raw-annotations false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genomicsdb-use-bcf-codec false --genomicsdb-shared-posixfs-optimizations false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false --allow-old-rms-mapping-quality-annotation-data false",Version="4.1.8.1",Date="September 15, 2021 3:30:43 PM CEST">
+##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --emit-ref-confidence GVCF --standard-min-confidence-threshold-for-calling 10.0 --output /ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/VARIANT_C0011JY/C0011JY_hs37d5_BOTH_01.HC.temp.g.vcf --intervals /ccc/work/cont007/fg/fg/biobank/by-soft/varscope/hs37d5/WG_hs37d5_regions.target_split_bed/01_overlap.bed --input /ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/MAPPING_C0011JY/reliable.realign.recal/A592_DA_C0011JY_H72NKCCX2_hs37d5_MERGE_PE_1_01.reliable.realign.recal.bam --reference /dev/shm/hs37d5_all_chr.fasta --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --adaptive-pruning false --do-not-recover-dangling-branches false --recover-dangling-heads false --consensus false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 1.0 --max-unpruned-variants 100 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --correct-overlapping-quality false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version=4.1.0.0,Date="August 4, 2020 4:14:40 PM CEST">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants">
+##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds of being a true variant versus being false under the trained gaussian mixture model">
+##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
+##bcftools_normCommand=norm -m - -w 10000 -f references/GRCh37/chr/hs37d5.fa; Date=Wed Sep 15 15:31:06 2021
+##bcftools_normVersion=1.12+htslib-1.12
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+##contig=<ID=NC_007605,length=171823>
+##contig=<ID=hs37d5,length=35477943>
+##reference=file:///dev/shm/hs37d5_all_chr.fasta
+##source=ApplyVQSR
+##source=GenomicsDBImport
+##source=GenotypeGVCFs
+##source=HaplotypeCaller
+##source=SelectVariants
+##bcftools_normCommand=norm -m - -w 1000 -c s -f references/GRCh37/chr/hs37d5.fa --threads 3 -Oz -o /pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/splitted/Dyslexia.gatk-vqsr.splitted.chr1.1-10000000.norm.vcf.gz; Date=Thu Sep 16 12:54:23 2021
+##VEP="v104" time="2021-09-16 12:54:40" cache="tools/ensembl-vep-104.3/data/homo_sapiens/104_GRCh37" ensembl-variation=104.20f5335 ensembl-funcgen=104.f1c7762 ensembl=104.1af1dce ensembl-io=104.1d3bb6e 1000genomes="phase3" COSMIC="92" ClinVar="202012" HGMD-PUBLIC="20204" assembly="GRCh37.p13" dbSNP="154" gencode="GENCODE 19" genebuild="2011-04" gnomAD="r2.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|CCDS|SIFT|PolyPhen|HGVS_OFFSET">
+##WARNING: 5 first names of the header of the initial file: CHROM POS REF ALT INFO
+##WARNING: if the 5 first columns of the .tsv file are not CHROM POS REF ALT INFO, then the .vcf file produced by this process is not good
+##INFO=<FISHER=GENE|IMPACT|CONSEQUENCE|AFF|UNAFF|OR|P_VALUE|NEG_LOG10_P_VALUE|PATIENT_NB|CSQ_TRANSCRIPT_NB|SIFT|PolyPhen|AC|AF>
+#CHROM POS ID REF ALT QUAL FILTER INFO
+chr1 10146 . AC A . . AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 2, 0: 3, 3: 1}|{0: 1, 1: 1}|1.0|1.0|-0.0|8|NA|NA|NA|7|0.3179999887943268
+chr1 10177 . A C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 1}|{}||1.0|-0.0|1|NA|NA|NA|1|0.0560000017285347
+chr1 10255 . A AAACCCTAACCCT . . AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{}|{}||1.0|-0.0|0|NA|NA|NA|2|0.20000000298023224
+chr1 10335 . AACCCTAACCCTAACCCT A . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=0.28200000524520874;DP=941;ExcessHet=3.0102999210357666;FS=6.5320000648498535;InbreedingCoeff=-0.08259999752044678;MLEAC=2;MLEAF=0.11100000143051147;MQ=36.91999816894531;MQRankSum=-1.7319999933242798;NEGATIVE_TRAIN_SITE=True;QD=4.409999847412109;ReadPosRankSum=-0.03500000014901161;SOR=0.01600000075995922;VQSLOD=-1.0399999618530273;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 1}|{}||1.0|-0.0|1|NA|NA|NA|1|0.0560000017285347
+chr1 10337 . CCCTAA C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=-0.14000000059604645;DP=1040;ExcessHet=3.0102999210357666;FS=0.0;InbreedingCoeff=0.34470000863075256;MLEAC=1;MLEAF=0.0560000017285347;MQ=37.65999984741211;MQRankSum=0.9670000076293945;NEGATIVE_TRAIN_SITE=True;QD=22.290000915527344;ReadPosRankSum=-1.593000054359436;SOR=1.6089999675750732;VQSLOD=-1.7790000438690186;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 4}|{0: 3}||1.0|-0.0|7|NA|NA|NA|1|0.0560000017285347
+chr1 10354 . C A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=-0.11400000005960464;DP=986;ExcessHet=3.0102999210357666;FS=10.295999526977539;InbreedingCoeff=-0.23739999532699585;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.619998931884766;MQRankSum=3.069999933242798;QD=14.640000343322754;ReadPosRankSum=1.2899999618530273;SOR=3.6040000915527344;VQSLOD=-16.719999313354492;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 1, 0: 1}|{}||1.0|-0.0|2|NA|NA|NA|1|0.04500000178813934
+chr1 10387 . T C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=1.1699999570846558;DP=1037;ExcessHet=3.0102999210357666;FS=1.9830000400543213;InbreedingCoeff=-0.2944999933242798;MLEAC=2;MLEAF=0.09099999815225601;MQ=32.439998626708984;MQRankSum=0.02800000086426735;QD=3.5399999618530273;ReadPosRankSum=-1.246000051498413;SOR=1.6089999675750732;VQSLOD=-7.425000190734863;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 1, 1: 1}|{}||1.0|-0.0|2|NA|NA|NA|1|0.04500000178813934
+chr1 10390 . CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=2.0899999141693115;DP=928;ExcessHet=3.0102999210357666;FS=3.2850000858306885;InbreedingCoeff=-0.2574000060558319;MLEAC=2;MLEAF=0.09099999815225601;MQ=37.08000183105469;MQRankSum=1.8700000047683716;NEGATIVE_TRAIN_SITE=True;QD=15.9399995803833;ReadPosRankSum=-2.8559999465942383;SOR=1.531999945640564;VQSLOD=-3.1649999618530273;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 2, 1: 1}|{}||1.0|-0.0|3|NA|NA|NA|1|0.04500000178813934
+chr1 10403 . ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A . . AC=1;AF=0.04500000178813934;AN=22;BaseQRankSum=0.9610000252723694;DP=861;ExcessHet=3.2221999168395996;FS=5.418000221252441;InbreedingCoeff=-0.12880000472068787;MLEAC=1;MLEAF=0.04500000178813934;MQ=41.47999954223633;MQRankSum=-1.0540000200271606;NEGATIVE_TRAIN_SITE=True;QD=1.5099999904632568;ReadPosRankSum=-0.35199999809265137;SOR=1.7389999628067017;VQSLOD=-1.9769999980926514;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{0: 5, 1: 1}|{0: 3}|inf|1.0|-0.0|9|NA|NA|NA|1|0.04500000178813934
diff --git a/example of results/PL_family_WGS_fisher_1663355226/vcf_csq_subfield_titles.txt b/example of results/PL_family_WGS_fisher_1663772349/vcf_csq_subfield_titles.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1663355226/vcf_csq_subfield_titles.txt
rename to example of results/PL_family_WGS_fisher_1663772349/vcf_csq_subfield_titles.txt
diff --git a/example of results/PL_family_WGS_fisher_1663355226/vcf_info_field_titles.txt b/example of results/PL_family_WGS_fisher_1663772349/vcf_info_field_titles.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1663355226/vcf_info_field_titles.txt
rename to example of results/PL_family_WGS_fisher_1663772349/vcf_info_field_titles.txt
diff --git a/example of results/PL_family_WGS_fisher_1663355634/fisher.tsv b/example of results/PL_family_WGS_fisher_1663773618/fisher.tsv
similarity index 99%
rename from example of results/PL_family_WGS_fisher_1663355634/fisher.tsv
rename to example of results/PL_family_WGS_fisher_1663773618/fisher.tsv
index 5e1427f..9f7b47b 100644
--- a/example of results/PL_family_WGS_fisher_1663355634/fisher.tsv
+++ b/example of results/PL_family_WGS_fisher_1663773618/fisher.tsv
@@ -1,4 +1,4 @@
-CHROM POS REF ALT INFO GENE SEVERITY IMPACT AFF UNAFF OR P_VALUE NEG_LOG10_P_VALUE PATIENT_NB CSQ_TRANSCRIPT_NB SIFT PolyPhen AC AF
+CHROM POS REF ALT INFO GENE IMPACT CONSEQUENCE AFF UNAFF OR P_VALUE NEG_LOG10_P_VALUE PATIENT_NB CSQ_TRANSCRIPT_NB SIFT PolyPhen AC AF
chr1 10146 AC A AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 2, 0: 3, 3: 1} {0: 1, 1: 1} 1.0 1.0 -0.0 8 NA NA NA 7 0.3179999887943268
chr1 10177 A C AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {1: 1} {} 1.0 -0.0 1 NA NA NA 1 0.0560000017285347
chr1 10255 A AAACCCTAACCCT AC=2;AF=0.20000000298023224;AN=10;DP=974;ExcessHet=0.24819999933242798;FS=0.0;InbreedingCoeff=0.2498999983072281;MLEAC=3;MLEAF=0.30000001192092896;MQ=27.06999969482422;QD=25.360000610351562;SOR=1.6089999675750732;VQSLOD=-0.6116999983787537;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| WASH7P MODIFIER downstream_gene_variant {} {} 1.0 -0.0 0 NA NA NA 2 0.20000000298023224
diff --git a/example of results/PL_family_WGS_fisher_1663773618/miami.png b/example of results/PL_family_WGS_fisher_1663773618/miami.png
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diff --git a/example of results/PL_family_WGS_fisher_1663355634/reports/Log_info.txt b/example of results/PL_family_WGS_fisher_1663773618/reports/Log_info.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1663355634/reports/Log_info.txt
rename to example of results/PL_family_WGS_fisher_1663773618/reports/Log_info.txt
diff --git a/example of results/PL_family_WGS_fisher_1663355634/reports/Run_info.txt b/example of results/PL_family_WGS_fisher_1663773618/reports/Run_info.txt
similarity index 89%
rename from example of results/PL_family_WGS_fisher_1663355634/reports/Run_info.txt
rename to example of results/PL_family_WGS_fisher_1663773618/reports/Run_info.txt
index 7329ae1..633eaa6 100644
--- a/example of results/PL_family_WGS_fisher_1663355634/reports/Run_info.txt
+++ b/example of results/PL_family_WGS_fisher_1663773618/reports/Run_info.txt
@@ -1,9 +1,9 @@
Project (empty means no .git folder where the main.nf file is present): origin git@gitlab.pasteur.fr:gmillot/fisher_for_vcf.git (fetch)
-Git info (empty means no .git folder where the main.nf file is present): 1.3-5-g2d3439c2ba-dirty
+Git info (empty means no .git folder where the main.nf file is present): v1.5-19-g5fa0e4463f-dirty
Cmd line: nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config -resume
execution mode: local
Manifest's pipeline version: null
-result path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1663355634
+result path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1663773618
nextflow version: 21.04.2
@@ -16,5 +16,5 @@ workDir (directory where tasks temporary files are created): /mnt/c/Users/Gael/D
USER VARIABLES:
-out_path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1663355634
+out_path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1663773618
sample_path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz
diff --git a/example of results/PL_family_WGS_fisher_1663355226/reports/dag.dot b/example of results/PL_family_WGS_fisher_1663773618/reports/dag.dot
similarity index 77%
rename from example of results/PL_family_WGS_fisher_1663355226/reports/dag.dot
rename to example of results/PL_family_WGS_fisher_1663773618/reports/dag.dot
index 57b1042..194d708 100644
--- a/example of results/PL_family_WGS_fisher_1663355226/reports/dag.dot
+++ b/example of results/PL_family_WGS_fisher_1663773618/reports/dag.dot
@@ -4,16 +4,16 @@ p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
p0 -> p1;
p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p25 [label="tsv2vcf"];
-p1 -> p25 [label="vcf_ch3"];
+p8 [label="vcf_subfield_title"];
+p1 -> p8 [label="vcf_ch1"];
p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p9 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="combine"];
-p1 -> p9 [label="vcf_ch2"];
+p24 [label="tsv2vcf"];
+p1 -> p24 [label="vcf_ch3"];
p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p8 [label="vcf_subfield_title"];
-p1 -> p8 [label="vcf_ch1"];
+p9 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="combine"];
+p1 -> p9 [label="vcf_ch2"];
p2 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.fromPath"];
p11 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="first"];
@@ -24,8 +24,8 @@ p10 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="first"];
p3 -> p10 [label="ped_ch"];
p4 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.fromPath"];
-p24 [label="miami_plot"];
-p4 -> p24 [label="chr_ch"];
+p23 [label="miami_plot"];
+p4 -> p23 [label="chr_ch"];
p5 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.from"];
p9 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="combine"];
@@ -68,51 +68,47 @@ p15 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
p14 -> p15;
p15 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p24 [label="miami_plot"];
-p15 -> p24 [label="fisher_ch3"];
+p24 [label="tsv2vcf"];
+p15 -> p24 [label="fisher_ch4"];
p15 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p16 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="subscribe"];
-p15 -> p16 [label="fisher_ch2"];
+p23 [label="miami_plot"];
+p15 -> p23 [label="fisher_ch3"];
p15 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p25 [label="tsv2vcf"];
-p15 -> p25 [label="fisher_ch4"];
+p16 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="subscribe"];
+p15 -> p16 [label="fisher_ch2"];
p17 [shape=point,label="",fixedsize=true,width=0.1];
-p24 [label="miami_plot"];
-p17 -> p24 [label="region_val"];
+p23 [label="miami_plot"];
+p17 -> p23 [label="x_lim_val"];
p18 [shape=point,label="",fixedsize=true,width=0.1];
-p24 [label="miami_plot"];
-p18 -> p24 [label="x_lim"];
+p23 [label="miami_plot"];
+p18 -> p23 [label="bottom_y_column"];
p19 [shape=point,label="",fixedsize=true,width=0.1];
-p24 [label="miami_plot"];
-p19 -> p24 [label="bottom_y_column"];
+p23 [label="miami_plot"];
+p19 -> p23 [label="color_column"];
p20 [shape=point,label="",fixedsize=true,width=0.1];
-p24 [label="miami_plot"];
-p20 -> p24 [label="color_column"];
+p23 [label="miami_plot"];
+p20 -> p23 [label="y_lim1"];
p21 [shape=point,label="",fixedsize=true,width=0.1];
-p24 [label="miami_plot"];
-p21 -> p24 [label="y_lim1"];
+p23 [label="miami_plot"];
+p21 -> p23 [label="y_lim2"];
p22 [shape=point,label="",fixedsize=true,width=0.1];
-p24 [label="miami_plot"];
-p22 -> p24 [label="y_lim2"];
+p23 [label="miami_plot"];
+p22 -> p23 [label="cute_file"];
-p23 [shape=point,label="",fixedsize=true,width=0.1];
-p24 [label="miami_plot"];
-p23 -> p24 [label="cute_file"];
+p25 [shape=point,label="",fixedsize=true,width=0.1];
+p27 [label="Backup"];
+p25 -> p27 [label="config_file"];
p26 [shape=point,label="",fixedsize=true,width=0.1];
-p28 [label="Backup"];
-p26 -> p28 [label="config_file"];
-
-p27 [shape=point,label="",fixedsize=true,width=0.1];
-p28 [label="Backup"];
-p27 -> p28 [label="log_file"];
+p27 [label="Backup"];
+p26 -> p27 [label="log_file"];
}
diff --git a/example of results/PL_family_WGS_fisher_1663355634/reports/fisher_for_vcf.config b/example of results/PL_family_WGS_fisher_1663773618/reports/fisher_for_vcf.config
similarity index 92%
rename from example of results/PL_family_WGS_fisher_1663355634/reports/fisher_for_vcf.config
rename to example of results/PL_family_WGS_fisher_1663773618/reports/fisher_for_vcf.config
index 28eff4c..158b1bf 100644
--- a/example of results/PL_family_WGS_fisher_1663355634/reports/fisher_for_vcf.config
+++ b/example of results/PL_family_WGS_fisher_1663773618/reports/fisher_for_vcf.config
@@ -23,11 +23,11 @@ env {
//chr_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/reference_genomes/human hg19_grch37/hg19_grch37p5_chr_size_cumul.txt" // human chromo infos
region = "none" // region to parse. Write "chr7:0-147000000, chr10:1000000-2000000" for a single region, "chr7:0-147000000, chr10:1000000-2000000" if two regions, ""chr7" for a whole chromosome, "chr7, chr1" for two chromosomes and "none" for the complete genome // Warning : replace eval() by ast.literal_eval() from ast package in the main py code ?
tsv_extra_fields = "AC AF CSQ_SIFT CSQ_PolyPhen" // subfields from INFO to add as columns in the tsv file. Example: tsv_extra_fields = "AC AF". Write "CSQ_PolyPhen" for a sub field of the CSQ field of INFO. Write "NULL" if not required
- x_lim = "region" // x-axis limits. Either "whole" for the whole genome, or "region" to have the x-axis limited to the region parameter. Not considered if region = "none"
+ x_lim = "chr1" // x-axis limits. Either "whole" for the whole genome, "region" to have the regions of the region parameter (i.e., "whole" if region == "none"), or a character string written like the region parameter, to have the x-axis limited to the x_lim parameter. Write "NULL" to does not plot results
bottom_y_column = "NULL" // any of the OR, P_VALUE, NEG_LOG10_P_VALUE or PATIENT_NB column of the res.tsv file for the y-axis of the bottom manhattan plot -> miami plot. Can also be an added column through the tsv_extra_fields parameter. Indicated column of field must be quantitative. Write "NULL" to get the res.tsv file and explore the columns before rerunning the nextflow process using - resume. "NULL" generates a simple manhattan plot
- color_column = "NULL" // as for bottom_y_column in order color the dots. Write "NULL" if not required (dots will be alternatively grey and blue, according to chromo order)
- y_lim1 = 5 // max y-axis limit of the top panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Write "NULL" for no particular limit
- y_lim2 = 20 // max y-axis limit of the bottom panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Not considered if bottom_y_column = "NULL"
+ color_column = "AF" // as for bottom_y_column in order color the dots. Write "NULL" if not required (dots will be alternatively grey and blue, according to chromo order)
+ y_lim1 = 3 // max y-axis limit of the top panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Write "NULL" for no particular limit
+ y_lim2 = 2 // max y-axis limit of the bottom panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Not considered if bottom_y_column = "NULL"
cute_path = "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.4.0/cute_little_R_functions.R" // single character string indicating the file (and absolute pathway) of the required cute_little_R_functions toolbox. With ethernet connection available, this can also be used: "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/raw/v5.1.0/cute_little_R_functions.R" or local "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
}
diff --git a/example of results/PL_family_WGS_fisher_1663355634/reports/fisher_report.txt b/example of results/PL_family_WGS_fisher_1663773618/reports/fisher_report.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1663355634/reports/fisher_report.txt
rename to example of results/PL_family_WGS_fisher_1663773618/reports/fisher_report.txt
diff --git a/example of results/PL_family_WGS_fisher_1663773618/reports/miami_report.txt b/example of results/PL_family_WGS_fisher_1663773618/reports/miami_report.txt
new file mode 100644
index 0000000..5840cfe
--- /dev/null
+++ b/example of results/PL_family_WGS_fisher_1663773618/reports/miami_report.txt
@@ -0,0 +1,129 @@
+
+
+################################################################ miami PROCESS
+
+
+
+
+
+
+################################ RUNNING DATE AND STARTING TIME
+
+
+
+
+2022-09-21 15:20:24
+
+
+
+
+
+
+################################ RUNNING
+
+
+
+
+
+
+################################ RUNNING END
+
+
+
+
+END TIME: 2022-09-21 15:20:25
+
+
+
+
+TOTAL TIME LAPSE: 2S
+
+
+
+
+ALL DATA SAVED IN all_objects.RData
+
+
+
+
+################################ RECAPITULATION OF WARNING MESSAGES
+
+
+
+
+NO WARNING MESSAGE TO REPORT
+
+
+
+
+################################ INITIAL SETTINGS OF PARAMETERS
+
+
+
+erase.objects TRUE
+erase.graphs TRUE
+script miami
+run.way SCRIPT
+command /usr/lib/R/bin/exec/R,--no-echo,--no-restore,--file=/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/bin/miami.R,--args,fisher.tsv,hg19_grch37p5_chr_size_cumul.txt,chr1,NULL,AF,3,2,cute_little_R_functions.R,miami_report.txt
+whole chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr23, chr24, chr25, chrY, chrX, chrM
+fisher fisher.tsv
+chr.path hg19_grch37p5_chr_size_cumul.txt
+x.lim chr1
+bottom.y.column NULL
+color.column AF
+y.lim1 3
+y.lim2 2
+cute cute_little_R_functions.R
+log miami_report.txt
+
+
+
+
+################################ R SYSTEM AND PACKAGES
+
+
+R version 4.1.2 (2021-11-01)
+Platform: x86_64-pc-linux-gnu (64-bit)
+Running under: Ubuntu 20.04.3 LTS
+
+Matrix products: default
+BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
+LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
+
+locale:
+ [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
+ [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
+ [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
+ [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
+ [9] LC_ADDRESS=C LC_TELEPHONE=C
+[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
+
+attached base packages:
+[1] stats graphics grDevices utils datasets methods base
+
+other attached packages:
+[1] ggplot2_3.3.3 lubridate_1.8.0 qqman_0.1.8
+
+loaded via a namespace (and not attached):
+ [1] assertthat_0.2.1 calibrate_1.7.7 cli_3.2.0 colorspace_2.0-3
+ [5] compiler_4.1.2 crayon_1.5.0 DBI_1.1.2 digest_0.6.29
+ [9] dplyr_1.0.8 ellipsis_0.3.2 fansi_1.0.2 farver_2.1.0
+[13] generics_0.1.2 glue_1.6.2 grid_4.1.2 gridExtra_2.3
+[17] gtable_0.3.0 labeling_0.4.2 lifecycle_1.0.1 magrittr_2.0.2
+[21] MASS_7.3-55 munsell_0.5.0 pillar_1.7.0 pkgconfig_2.0.3
+[25] purrr_0.3.4 R6_2.5.1 rlang_1.0.2 scales_1.1.1
+[29] tibble_3.1.6 tidyselect_1.1.2 utf8_1.2.2 vctrs_0.3.8
+[33] withr_2.5.0
+
+
+
+
+
+################################ JOB END
+
+TIME: 2022-09-21 15:20:25
+
+TOTAL TIME LAPSE: 2S
+
+
+
diff --git a/example of results/PL_family_WGS_fisher_1663355634/reports/report.html b/example of results/PL_family_WGS_fisher_1663773618/reports/report.html
similarity index 99%
rename from example of results/PL_family_WGS_fisher_1663355634/reports/report.html
rename to example of results/PL_family_WGS_fisher_1663773618/reports/report.html
index 7083206..ece84ce 100644
--- a/example of results/PL_family_WGS_fisher_1663355634/reports/report.html
+++ b/example of results/PL_family_WGS_fisher_1663773618/reports/report.html
@@ -18,11 +18,11 @@
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
- <meta name="description" content="Nextflow workflow report for run id [distracted_golick]">
+ <meta name="description" content="Nextflow workflow report for run id [nostalgic_davinci]">
<meta name="author" content="Paolo Di Tommaso, Phil Ewels">
<link rel="icon" type="image/png" href="https://www.nextflow.io/img/favicon.png" />
- <title>[distracted_golick] Nextflow Workflow Report</title>
+ <title>[nostalgic_davinci] Nextflow Workflow Report</title>
<style type="text/css">
/*!
@@ -137,7 +137,7 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r
<li class="nav-item"><a class="nav-link" href="#tasks">Tasks</a></li>
</ul>
<span class="navbar-text">
- [distracted_golick]
+ [nostalgic_davinci]
</span>
</div>
</nav>
@@ -146,58 +146,27 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r
<div class="container">
<h1 class="display-3">Nextflow workflow report</h1>
- <h2 class="text-muted mb-4"><samp>[distracted_golick]</samp> <em>(resumed run)</em></h2>
+ <h2 class="text-muted mb-4"><samp>[nostalgic_davinci]</samp> <em>(resumed run)</em></h2>
- <div class="alert alert-danger mb-4">
- <h4>Workflow execution completed unsuccessfully!</h4>
- <p>The exit status of the task that caused the workflow execution to fail was: <code>1</code>.</p>
- <p>The full error message was:</p>
- <pre>Error executing process > 'miami_plot (1)'
-
-Caused by:
- Process `miami_plot (1)` terminated with an error exit status (1)
-
-Command executed:
-
- #!/bin/bash -ue
- miami.R fisher.tsv hg19_grch37p5_chr_size_cumul.txt "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr23, chr24, chr25, chrY, chrX, chrM" "region" "NULL" "NULL" "5" "20" "cute_little_R_functions.R" "miami_report.txt"
-
-Command exit status:
- 1
-
-Command output:
-
-
- KIND OF RUN (SCRIPT, COPY-PASTE OR SOURCE): SCRIPT
-
-Command error:
- Error in if (any(diff(tempo) < 0)) { :
- missing value where TRUE/FALSE needed
- In addition: Warning message:
- NAs introduced by coercion
- Execution halted
-
-Work dir:
- /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/work/e7/19507ac0b76cd98a52eed1273c948c
-
-Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line</pre>
+ <div class="alert alert-success mb-4">
+ Workflow execution completed successfully!
</div>
<dl>
<dt>Run times</dt>
<dd>
- <span id="workflow_start">16-Sep-2022 21:13:55</span> - <span id="workflow_complete">16-Sep-2022 21:16:07</span>
- (<span id="completed_fromnow"></span>duration: <strong>2m 13s</strong>)
+ <span id="workflow_start">21-Sep-2022 17:20:18</span> - <span id="workflow_complete">21-Sep-2022 17:20:26</span>
+ (<span id="completed_fromnow"></span>duration: <strong>7.8s</strong>)
</dd>
<dl>
<div class="progress" style="height: 1.6rem; margin: 1.2rem auto; border-radius: 0.20rem;">
- <div style="width: 66.67%" class="progress-bar bg-success" data-toggle="tooltip" data-placement="top" title="4 tasks succeeded"><span class="text-truncate"> 4 succeeded </span></div>
- <div style="width: 16.67%" class="progress-bar bg-secondary" data-toggle="tooltip" data-placement="top" title="1 tasks were cached"><span class="text-truncate"> 1 cached </span></div>
+ <div style="width: 50.0%" class="progress-bar bg-success" data-toggle="tooltip" data-placement="top" title="3 tasks succeeded"><span class="text-truncate"> 3 succeeded </span></div>
+ <div style="width: 50.0%" class="progress-bar bg-secondary" data-toggle="tooltip" data-placement="top" title="3 tasks were cached"><span class="text-truncate"> 3 cached </span></div>
<div style="width: 0.0%" class="progress-bar bg-warning" data-toggle="tooltip" data-placement="top" title="0 tasks reported and error and were ignored"><span class="text-truncate"> 0 ignored </span></div>
- <div style="width: 16.67%" class="progress-bar bg-danger" data-toggle="tooltip" data-placement="top" title="1 tasks failed"><span class="text-truncate"> 1 failed </span></div>
+ <div style="width: 0.0%" class="progress-bar bg-danger" data-toggle="tooltip" data-placement="top" title="0 tasks failed"><span class="text-truncate"> 0 failed </span></div>
</div>
</dl>
@@ -207,7 +176,7 @@ Tip: when you have fixed the problem you can continue the execution adding the o
<dl class="row small">
<dt class="col-sm-3">CPU-Hours</dt>
- <dd class="col-sm-9"><samp>0.6 (0.1% cached, 0.2% failed)</samp></dd>
+ <dd class="col-sm-9"><samp>0.5 (99.4% cached)</samp></dd>
<dt class="col-sm-3">Launch directory</dt>
<dd class="col-sm-9"><samp>/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf</samp></dd>
@@ -225,11 +194,11 @@ Tip: when you have fixed the problem you can continue the execution adding the o
<dt class="col-sm-3">Script ID</dt>
- <dd class="col-sm-9"><code>6e134d4f75f8aa0cf8d733c9e9c37df5</code></dd>
+ <dd class="col-sm-9"><code>f8aa46e0a332e25923ce89b43f2c6938</code></dd>
<dt class="col-sm-3">Workflow session</dt>
- <dd class="col-sm-9"><code>22359bce-ba4e-42e0-8d98-e97ed57f40f8</code></dd>
+ <dd class="col-sm-9"><code>20070b19-406b-4731-b65a-fb45186895de</code></dd>
@@ -1060,7 +1029,7 @@ $(function() {
// Nextflow report data
window.data = { "trace":[
-{"task_id":"1","hash":"36\/992bb0","native_id":"4312","process":"WorkflowVersion","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"WorkflowVersion","status":"COMPLETED","exit":"0","submit":"1663355636542","start":"1663355636567","complete":"1663355637588","duration":"1046","realtime":"365","%cpu":"18.6","%mem":"0.0","rss":"3346432","vmem":"20148224","peak_rss":"3346432","peak_vmem":"20148224","rchar":"136970","wchar":"1547","syscr":"270","syscw":"35","read_bytes":"3466240","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/36\/992bb041bf6b2582b5c9cda27e5fbb","script":"\n echo \"Project (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf remote -v | head -n 1) > Run_info.txt # works only if the main script run is located in a directory that has a .git folder, i.e., that is connected to a distant repo\n echo \"Git info (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf describe --abbrev=10 --dirty --always --tags) >> Run_info.txt # idem. Provide the small commit number of the script and nextflow.config used in the execution\n echo \"Cmd line: nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config -resume\" >> Run_info.txt\n echo \"execution mode\": local >> Run_info.txt\n modules= # this is just to deal with variable interpretation during the creation of the .command.sh file by nextflow. See also $modules below\n if [[ ! -z $modules ]] ; then\n echo \"loaded modules (according to specification by the user thanks to the --modules argument of main.nf)\": >> Run_info.txt\n fi\n echo \"Manifest\'s pipeline version: null\" >> Run_info.txt\n echo \"result path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663355634\" >> Run_info.txt\n echo \"nextflow version: 21.04.2\" >> Run_info.txt\n echo -e \"\\n\\nIMPLICIT VARIABLES:\\n\\nlaunchDir (directory where the workflow is run): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nprojectDir (directory where the main.nf script is located): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nworkDir (directory where tasks temporary files are created): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\" >> Run_info.txt\n echo -e \"\\n\\nUSER VARIABLES:\\n\\nout_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663355634\\nsample_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\" >> Run_info.txt\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=region\nbottom_y_column=NULL\ncolor_column=NULL\ny_lim1=5\ny_lim2=20\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663355634\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"17","inv_ctxt":"0"},{"task_id":"2","hash":"8c\/70ebc8","native_id":"22603","process":"vcf_subfield_title","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-r_v4.1.2_extended_v2.1-gitlab_v8.8.img","tag":"-","name":"vcf_subfield_title (1)","status":"CACHED","exit":"0","submit":"1663352738989","start":"1663352739078","complete":"1663352742379","duration":"3390","realtime":"2825","%cpu":"46.0","%mem":"0.1","rss":"108023808","vmem":"230711296","peak_rss":"108023808","peak_vmem":"230744064","rchar":"12700786","wchar":"3171","syscr":"1666","syscw":"243","read_bytes":"16723968","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/8c\/70ebc82f28496fe0f9396ba210ad79","script":"\n #!\/bin\/bash -ue\n vcf_subfield_title.R Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz \"cute_little_R_functions.R\" \"miami_report.txt\"\n ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen CSQ_Feature\nx_lim=region\nbottom_y_column=NULL\ncolor_column=NULL\ny_lim1=5\ny_lim2=20\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663352735\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"6889","inv_ctxt":"4"},{"task_id":"3","hash":"e1\/71e067","native_id":"4524","process":"Backup","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"Backup","status":"COMPLETED","exit":"0","submit":"1663355637612","start":"1663355637689","complete":"1663355638228","duration":"616","realtime":"7","%cpu":"21.8","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"106721","wchar":"342","syscr":"189","syscw":"14","read_bytes":"329728","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/e1\/71e067eea2bd73ed84867e9058ee8e","script":"\n echo -e \"full .nextflow.log is in: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nThe one in the result folder is not complete (miss the end)\" > Log_info.txt\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=region\nbottom_y_column=NULL\ncolor_column=NULL\ny_lim1=5\ny_lim2=20\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663355634\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"4","hash":"c1\/38d1e9","native_id":"4653","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (1)","status":"COMPLETED","exit":"0","submit":"1663355638238","start":"1663355638327","complete":"1663355760799","duration":"122561","realtime":"122051","%cpu":"55.8","%mem":"0.2","rss":"191180800","vmem":"1514635264","peak_rss":"192217088","peak_vmem":"1515585536","rchar":"17383057","wchar":"13700507","syscr":"2067","syscw":"1951","read_bytes":"53187584","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/c1\/38d1e965c7497c1f2cde8622c722a4","script":"\n #!\/bin\/bash -ue\n fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr1\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" \"vcf_csq_subfield_titles.txt\" \"fisher_report.txt\"\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=region\nbottom_y_column=NULL\ncolor_column=NULL\ny_lim1=5\ny_lim2=20\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663355634\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"618339","inv_ctxt":"1581"},{"task_id":"6","hash":"6b\/7e6ceb","native_id":"6575","process":"tsv2vcf","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"tsv2vcf (1)","status":"COMPLETED","exit":"0","submit":"1663355761338","start":"1663355761400","complete":"1663355764338","duration":"3000","realtime":"2405","%cpu":"26.1","%mem":"0.0","rss":"6889472","vmem":"44240896","peak_rss":"6889472","peak_vmem":"44240896","rchar":"13922878","wchar":"13953971","syscr":"1898","syscw":"18229","read_bytes":"582656","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/6b\/7e6ceb7082b681ee470cff10e0ebb4","script":"\n #!\/bin\/bash -ue\n PREHEADER=\'##fileformat=VCFv4.2;build by fisher_for_vcf.nf\\n##WARNING: This file is not a true VCF since FORMAT AND sample (indiv) columns are not present\'\n HEADER=\'#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\'\n echo -e $PREHEADER > res.vcf\n FILENAME=$(basename -- \"Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\") # recover a file name without path\n FILE_EXTENSION=\"${FILENAME##*.}\" # ## means \"delete the longest regex starting at the beginning of the tested string\". If nothing, delete nothing. Thus ##*. means delete the longest string finishing by a dot. Use # instead of ## for \"delete the shortest regex starting at the beginning of the tested string\"\n if [[ \"${FILE_EXTENSION}\" =~ gz ]] ; then\n zcat Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz | awk \'{\n if($0 ~ \"^##.*\"){\n print $0\n }else{\n exit 0\n }\n }\' >> res.vcf\n else\n awk \'{\n if($0 ~ \"^##.*\"){\n print $0\n }else{\n exit 0\n }\n }\' Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz >> res.vcf\n fi\n awk -v var1=$HEADER \'BEGIN{FS=\"\\t\" ; OFS=\"\" ; ORS=\"\"}\n NR==1{\n print \"##WARNING: 5 first names of the header of the initial file: \"$1\" \"$2\" \"$3\" \"$4\" \"$5\"\\n\" ;\n print \"##WARNING: if the 5 first columns of the .tsv file are not CHROM POS REF ALT INFO, then the .vcf file produced by this process is not good\\n\" ;\n print \"##INFO=<FISHER=\" ;\n for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n print \">\\n\" ;\n print var1\"\\n\"\n }\n NR > 1{\n gsub(\"[\\\\[\\\\]\\\'\"\'\"\']\", \"\", $4)\n print $1\"\\t\"$2\"\\t.\\t\"$3\"\\t\"$4\"\\t.\\t.\\t\"$5\";FISHER=\" ;\n for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n print \"\\n\"\n }\n \' fisher.tsv >> res.vcf\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=region\nbottom_y_column=NULL\ncolor_column=NULL\ny_lim1=5\ny_lim2=20\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663355634\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"18154","inv_ctxt":"16"},{"task_id":"5","hash":"e7\/19507a","native_id":"6868","process":"miami_plot","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-r_v4.1.2_extended_v2.1-gitlab_v8.8.img","tag":"-","name":"miami_plot (1)","status":"FAILED","exit":"1","submit":"1663355764347","start":"1663355764438","complete":"1663355767779","duration":"3432","realtime":"3341","%cpu":"-","%mem":"-","rss":"-","vmem":"-","peak_rss":"-","peak_vmem":"-","rchar":"-","wchar":"-","syscr":"-","syscw":"-","read_bytes":"-","write_bytes":"-","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/e7\/19507ac0b76cd98a52eed1273c948c","script":"\n #!\/bin\/bash -ue\n miami.R fisher.tsv hg19_grch37p5_chr_size_cumul.txt \"chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr23, chr24, chr25, chrY, chrX, chrM\" \"region\" \"NULL\" \"NULL\" \"5\" \"20\" \"cute_little_R_functions.R\" \"miami_report.txt\"\n ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=region\nbottom_y_column=NULL\ncolor_column=NULL\ny_lim1=5\ny_lim2=20\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663355634\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"TERMINATE","vol_ctxt":"-","inv_ctxt":"-"}], 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+{"task_id":"1","hash":"c0\/e6c03b","native_id":"7462","process":"WorkflowVersion","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"WorkflowVersion","status":"COMPLETED","exit":"0","submit":"1663773619971","start":"1663773620022","complete":"1663773621157","duration":"1186","realtime":"456","%cpu":"15.6","%mem":"0.0","rss":"5029888","vmem":"40296448","peak_rss":"5029888","peak_vmem":"40296448","rchar":"148505","wchar":"6665","syscr":"275","syscw":"36","read_bytes":"3183616","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/c0\/e6c03b98e29edbf47ad264080b1814","script":"\n echo \"Project (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf remote -v | head -n 1) > Run_info.txt # works only if the main script run is located in a directory that has a .git folder, i.e., that is connected to a distant repo\n echo \"Git info (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf describe --abbrev=10 --dirty --always --tags) >> Run_info.txt # idem. Provide the small commit number of the script and nextflow.config used in the execution\n echo \"Cmd line: nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config -resume\" >> Run_info.txt\n echo \"execution mode\": local >> Run_info.txt\n modules= # this is just to deal with variable interpretation during the creation of the .command.sh file by nextflow. See also $modules below\n if [[ ! -z $modules ]] ; then\n echo \"loaded modules (according to specification by the user thanks to the --modules argument of main.nf)\": >> Run_info.txt\n fi\n echo \"Manifest\'s pipeline version: null\" >> Run_info.txt\n echo \"result path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663773618\" >> Run_info.txt\n echo \"nextflow version: 21.04.2\" >> Run_info.txt\n echo -e \"\\n\\nIMPLICIT VARIABLES:\\n\\nlaunchDir (directory where the workflow is run): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nprojectDir (directory where the main.nf script is located): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nworkDir (directory where tasks temporary files are created): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\" >> Run_info.txt\n echo -e \"\\n\\nUSER VARIABLES:\\n\\nout_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663773618\\nsample_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\" >> Run_info.txt\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663773618\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"14","inv_ctxt":"23"},{"task_id":"2","hash":"cb\/691615","native_id":"10420","process":"vcf_subfield_title","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-r_v4.1.2_extended_v2.1-gitlab_v8.8.img","tag":"-","name":"vcf_subfield_title (1)","status":"CACHED","exit":"0","submit":"1663601182550","start":"1663601182632","complete":"1663601186133","duration":"3583","realtime":"3114","%cpu":"40.8","%mem":"0.1","rss":"110145536","vmem":"230440960","peak_rss":"110145536","peak_vmem":"230473728","rchar":"12700654","wchar":"3162","syscr":"1666","syscw":"243","read_bytes":"16934912","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/cb\/6916153b9e5ccba99ba84e8072dcf8","script":"\n #!\/bin\/bash -ue\n vcf_subfield_title.R Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz \"cute_little_R_functions.R\" \"miami_report.txt\"\n ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=region\nbottom_y_column=NULL\ncolor_column=NULL\ny_lim1=5\ny_lim2=20\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663601179\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"9761","inv_ctxt":"4"},{"task_id":"4","hash":"66\/e5e2d0","native_id":"2680","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (1)","status":"CACHED","exit":"0","submit":"1663771934818","start":"1663771934907","complete":"1663772050507","duration":"115689","realtime":"115205","%cpu":"56.2","%mem":"0.2","rss":"189751296","vmem":"1512558592","peak_rss":"191893504","peak_vmem":"1514913792","rchar":"17391159","wchar":"13700500","syscr":"2072","syscw":"1951","read_bytes":"52996096","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/66\/e5e2d030668adb86c4d92e426d50c3","script":"\n #!\/bin\/bash -ue\n fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr1\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" \"vcf_csq_subfield_titles.txt\" \"fisher_report.txt\"\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=NULL\nbottom_y_column=AF\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663771931\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"600876","inv_ctxt":"1653"},{"task_id":"5","hash":"6b\/1cdea0","native_id":"4494","process":"tsv2vcf","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"tsv2vcf (1)","status":"CACHED","exit":"0","submit":"1663772051021","start":"1663772051108","complete":"1663772053867","duration":"2846","realtime":"2257","%cpu":"27.8","%mem":"0.0","rss":"6926336","vmem":"44236800","peak_rss":"6926336","peak_vmem":"44236800","rchar":"13922734","wchar":"13949868","syscr":"1897","syscw":"18238","read_bytes":"582656","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/6b\/1cdea041488efc5ca23ef84dcaaa08","script":"\n #!\/bin\/bash -ue\n PREHEADER=\'##fileformat=VCFv4.2;build by fisher_for_vcf.nf\\n##WARNING: This file is not a true VCF since FORMAT AND sample (indiv) columns are not present\'\n HEADER=\'#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\'\n echo -e $PREHEADER > res.vcf\n FILENAME=$(basename -- \"Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\") # recover a file name without path\n FILE_EXTENSION=\"${FILENAME##*.}\" # ## means \"delete the longest regex starting at the beginning of the tested string\". If nothing, delete nothing. Thus ##*. means delete the longest string finishing by a dot. Use # instead of ## for \"delete the shortest regex starting at the beginning of the tested string\"\n if [[ \"${FILE_EXTENSION}\" =~ gz ]] ; then\n zcat Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz | awk \'{\n if($0 ~ \"^##.*\"){\n print $0\n }else{\n exit 0\n }\n }\' >> res.vcf\n else\n awk \'{\n if($0 ~ \"^##.*\"){\n print $0\n }else{\n exit 0\n }\n }\' Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz >> res.vcf\n fi\n awk -v var1=$HEADER \'BEGIN{FS=\"\\t\" ; OFS=\"\" ; ORS=\"\"}\n NR==1{\n print \"##WARNING: 5 first names of the header of the initial file: \"$1\" \"$2\" \"$3\" \"$4\" \"$5\"\\n\" ;\n print \"##WARNING: if the 5 first columns of the .tsv file are not CHROM POS REF ALT INFO, then the .vcf file produced by this process is not good\\n\" ;\n print \"##INFO=<FISHER=\" ;\n for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n print \">\\n\" ;\n print var1\"\\n\"\n }\n NR > 1{\n gsub(\"[\\\\[\\\\]\\\'\"\'\"\']\", \"\", $4)\n print $1\"\\t\"$2\"\\t.\\t\"$3\"\\t\"$4\"\\t.\\t.\\t\"$5\";FISHER=\" ;\n for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n print \"\\n\"\n }\n \' fisher.tsv >> res.vcf\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=NULL\nbottom_y_column=AF\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663771931\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"18972","inv_ctxt":"12"},{"task_id":"3","hash":"1a\/54a330","native_id":"7676","process":"Backup","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"Backup","status":"COMPLETED","exit":"0","submit":"1663773621170","start":"1663773621257","complete":"1663773621747","duration":"577","realtime":"5","%cpu":"25.4","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"106581","wchar":"332","syscr":"189","syscw":"14","read_bytes":"329728","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/1a\/54a330093147b090a44958fd657fd8","script":"\n echo -e \"full .nextflow.log is in: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nThe one in the result folder is not complete (miss the end)\" > Log_info.txt\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663773618\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"6","hash":"7b\/b59ac4","native_id":"7807","process":"miami_plot","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-r_v4.1.2_extended_v2.1-gitlab_v8.8.img","tag":"-","name":"miami_plot (1)","status":"COMPLETED","exit":"0","submit":"1663773621758","start":"1663773621847","complete":"1663773626248","duration":"4490","realtime":"4016","%cpu":"59.6","%mem":"0.2","rss":"192413696","vmem":"334729216","peak_rss":"192413696","peak_vmem":"334856192","rchar":"28603666","wchar":"85585","syscr":"5938","syscw":"225","read_bytes":"42497024","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/7b\/b59ac40564c5d9a97384e0a2882ee4","script":"\n #!\/bin\/bash -ue\n miami.R fisher.tsv hg19_grch37p5_chr_size_cumul.txt \"chr1\" \"NULL\" \"AF\" \"3\" \"2\" \"cute_little_R_functions.R\" \"miami_report.txt\"\n ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1663773618\nsystem_exec=local\nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"5888","inv_ctxt":"19"}], "summary":[{"cpuUsage":{"mean":40.8,"min":40.8,"q1":40.8,"q2":40.8,"q3":40.8,"max":40.8,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title (1)"},"process":"vcf_subfield_title","mem":{"mean":110145536,"min":110145536,"q1":110145536,"q2":110145536,"q3":110145536,"max":110145536,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title (1)"},"memUsage":{"mean":0.16,"min":0.16,"q1":0.16,"q2":0.16,"q3":0.16,"max":0.16,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title (1)"},"timeUsage":null,"vmem":{"mean":230473728,"min":230473728,"q1":230473728,"q2":230473728,"q3":230473728,"max":230473728,"minLabel":"vcf_subfield_title 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</script>
diff --git a/example of results/PL_family_WGS_fisher_1663355634/reports/timeline.html b/example of results/PL_family_WGS_fisher_1663773618/reports/timeline.html
similarity index 99%
rename from example of results/PL_family_WGS_fisher_1663355634/reports/timeline.html
rename to example of results/PL_family_WGS_fisher_1663773618/reports/timeline.html
index 2386e41..1ee5f42 100644
--- a/example of results/PL_family_WGS_fisher_1663355634/reports/timeline.html
+++ b/example of results/PL_family_WGS_fisher_1663773618/reports/timeline.html
@@ -205,16 +205,16 @@ $(function() {
// Nextflow report data
window.data = {
- "elapsed": "2m 13s",
- "beginningMillis": 1663352738989,
- "endingMillis": 1663355768449,
+ "elapsed": "8.1s",
+ "beginningMillis": 1663601182550,
+ "endingMillis": 1663773626770,
"processes": [
- {"label": "WorkflowVersion", "cached": false, "index": 0, "times": [{"starting_time": 1663355636542, "ending_time": 1663355636567}, {"starting_time": 1663355636567, "ending_time": 1663355636932, "label": "1s \/ 3.2 MB"}, {"starting_time": 1663355636932, "ending_time": 1663355637588}]},
- {"label": "vcf_subfield_title (1)", "cached": true, "index": 1, "times": [{"starting_time": 1663352738989, "ending_time": 1663352739078}, {"starting_time": 1663352739078, "ending_time": 1663352741903, "label": "3.4s \/ 103 MB \/ CACHED"}, {"starting_time": 1663352741903, "ending_time": 1663352742379}]},
- {"label": "Backup", "cached": false, "index": 2, "times": [{"starting_time": 1663355637612, "ending_time": 1663355637689}, {"starting_time": 1663355637689, "ending_time": 1663355637696, "label": "616ms \/ 0"}, {"starting_time": 1663355637696, "ending_time": 1663355638228}]},
- {"label": "fisher (1)", "cached": false, "index": 3, "times": [{"starting_time": 1663355638238, "ending_time": 1663355638327}, {"starting_time": 1663355638327, "ending_time": 1663355760378, "label": "2m 3s \/ 183.3 MB"}, {"starting_time": 1663355760378, "ending_time": 1663355760799}]},
- {"label": "tsv2vcf (1)", "cached": false, "index": 4, "times": [{"starting_time": 1663355761338, "ending_time": 1663355761400}, {"starting_time": 1663355761400, "ending_time": 1663355763805, "label": "3s \/ 6.6 MB"}, {"starting_time": 1663355763805, "ending_time": 1663355764338}]},
- {"label": "miami_plot (1)", "cached": false, "index": 5, "times": [{"starting_time": 1663355764347, "ending_time": 1663355764438}, {"starting_time": 1663355764438, "ending_time": 1663355767779, "label": "3.4s \/ -"}]}
+ {"label": "WorkflowVersion", "cached": false, "index": 0, "times": [{"starting_time": 1663773619971, "ending_time": 1663773620022}, {"starting_time": 1663773620022, "ending_time": 1663773620478, "label": "1.2s \/ 4.8 MB"}, {"starting_time": 1663773620478, "ending_time": 1663773621157}]},
+ {"label": "vcf_subfield_title (1)", "cached": true, "index": 1, "times": [{"starting_time": 1663601182550, "ending_time": 1663601182632}, {"starting_time": 1663601182632, "ending_time": 1663601185746, "label": "3.6s \/ 105 MB \/ CACHED"}, {"starting_time": 1663601185746, "ending_time": 1663601186133}]},
+ {"label": "fisher (1)", "cached": true, "index": 2, "times": [{"starting_time": 1663771934818, "ending_time": 1663771934907}, {"starting_time": 1663771934907, "ending_time": 1663772050112, "label": "1m 56s \/ 183 MB \/ CACHED"}, {"starting_time": 1663772050112, "ending_time": 1663772050507}]},
+ {"label": "tsv2vcf (1)", "cached": true, "index": 3, "times": [{"starting_time": 1663772051021, "ending_time": 1663772051108}, {"starting_time": 1663772051108, "ending_time": 1663772053365, "label": "2.8s \/ 6.6 MB \/ CACHED"}, {"starting_time": 1663772053365, "ending_time": 1663772053867}]},
+ {"label": "Backup", "cached": false, "index": 4, "times": [{"starting_time": 1663773621170, "ending_time": 1663773621257}, {"starting_time": 1663773621257, "ending_time": 1663773621262, "label": "577ms \/ 0"}, {"starting_time": 1663773621262, "ending_time": 1663773621747}]},
+ {"label": "miami_plot (1)", "cached": false, "index": 5, "times": [{"starting_time": 1663773621758, "ending_time": 1663773621847}, {"starting_time": 1663773621847, "ending_time": 1663773625863, "label": "4.5s \/ 183.5 MB"}, {"starting_time": 1663773625863, "ending_time": 1663773626248}]}
]
}
;
diff --git a/example of results/PL_family_WGS_fisher_1663773618/reports/trace.txt b/example of results/PL_family_WGS_fisher_1663773618/reports/trace.txt
new file mode 100644
index 0000000..445ea9b
--- /dev/null
+++ b/example of results/PL_family_WGS_fisher_1663773618/reports/trace.txt
@@ -0,0 +1,7 @@
+task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
+2 cb/691615 10420 vcf_subfield_title (1) CACHED 0 2022-09-19 17:26:22.550 3.6s 3.1s 40.8% 105 MB 219.8 MB 12.1 MB 3.1 KB
+4 66/e5e2d0 2680 fisher (1) CACHED 0 2022-09-21 16:52:14.818 1m 56s 1m 55s 56.2% 183 MB 1.4 GB 16.6 MB 13.1 MB
+5 6b/1cdea0 4494 tsv2vcf (1) CACHED 0 2022-09-21 16:54:11.021 2.8s 2.3s 27.8% 6.6 MB 42.2 MB 13.3 MB 13.3 MB
+1 c0/e6c03b 7462 WorkflowVersion COMPLETED 0 2022-09-21 17:20:19.971 1.2s 456ms 15.6% 4.8 MB 38.4 MB 145 KB 6.5 KB
+3 1a/54a330 7676 Backup COMPLETED 0 2022-09-21 17:20:21.170 577ms 5ms 25.4% 0 0 104.1 KB 332 B
+6 7b/b59ac4 7807 miami_plot (1) COMPLETED 0 2022-09-21 17:20:21.758 4.5s 4s 59.6% 183.5 MB 319.3 MB 27.3 MB 83.6 KB
diff --git a/example of results/PL_family_WGS_fisher_1663355634/res.vcf b/example of results/PL_family_WGS_fisher_1663773618/res.vcf
similarity index 99%
rename from example of results/PL_family_WGS_fisher_1663355634/res.vcf
rename to example of results/PL_family_WGS_fisher_1663773618/res.vcf
index 0bee978..d75c96f 100644
--- a/example of results/PL_family_WGS_fisher_1663355634/res.vcf
+++ b/example of results/PL_family_WGS_fisher_1663773618/res.vcf
@@ -148,7 +148,7 @@
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|CCDS|SIFT|PolyPhen|HGVS_OFFSET">
##WARNING: 5 first names of the header of the initial file: CHROM POS REF ALT INFO
##WARNING: if the 5 first columns of the .tsv file are not CHROM POS REF ALT INFO, then the .vcf file produced by this process is not good
-##INFO=<FISHER=GENE|SEVERITY|IMPACT|AFF|UNAFF|OR|P_VALUE|NEG_LOG10_P_VALUE|PATIENT_NB|CSQ_TRANSCRIPT_NB|SIFT|PolyPhen|AC|AF>
+##INFO=<FISHER=GENE|IMPACT|CONSEQUENCE|AFF|UNAFF|OR|P_VALUE|NEG_LOG10_P_VALUE|PATIENT_NB|CSQ_TRANSCRIPT_NB|SIFT|PolyPhen|AC|AF>
#CHROM POS ID REF ALT QUAL FILTER INFO
chr1 10146 . AC A . . AC=7;AF=0.3179999887943268;AN=22;BaseQRankSum=0.3409999907016754;DB=True;DP=1004;ExcessHet=0.5741999745368958;FS=32.034000396728516;InbreedingCoeff=0.259799987077713;MLEAC=7;MLEAF=0.3179999887943268;MQ=35.310001373291016;MQRankSum=-0.40299999713897705;QD=10.390000343322754;ReadPosRankSum=1.0199999809265137;SOR=3.687000036239624;VQSLOD=1.659999966621399;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 2, 0: 3, 3: 1}|{0: 1, 1: 1}|1.0|1.0|-0.0|8|NA|NA|NA|7|0.3179999887943268
chr1 10177 . A C . . AC=1;AF=0.0560000017285347;AN=18;BaseQRankSum=1.7200000286102295;DB=True;DP=823;ExcessHet=3.0102999210357666;FS=4.301000118255615;InbreedingCoeff=-0.18729999661445618;MLEAC=3;MLEAF=0.16699999570846558;MQ=32.119998931884766;MQRankSum=1.6799999475479126;QD=13.289999961853027;ReadPosRankSum=1.0099999904632568;SOR=2.8329999446868896;VQSLOD=-11.149999618530273;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||;FISHER=WASH7P|MODIFIER|downstream_gene_variant|{1: 1}|{}||1.0|-0.0|1|NA|NA|NA|1|0.0560000017285347
diff --git a/example of results/PL_family_WGS_fisher_1663355634/vcf_csq_subfield_titles.txt b/example of results/PL_family_WGS_fisher_1663773618/vcf_csq_subfield_titles.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1663355634/vcf_csq_subfield_titles.txt
rename to example of results/PL_family_WGS_fisher_1663773618/vcf_csq_subfield_titles.txt
diff --git a/example of results/PL_family_WGS_fisher_1663355634/vcf_info_field_titles.txt b/example of results/PL_family_WGS_fisher_1663773618/vcf_info_field_titles.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1663355634/vcf_info_field_titles.txt
rename to example of results/PL_family_WGS_fisher_1663773618/vcf_info_field_titles.txt
diff --git a/fisher_for_vcf.config b/fisher_for_vcf.config
index 7c6e5e4..158b1bf 100644
--- a/fisher_for_vcf.config
+++ b/fisher_for_vcf.config
@@ -23,8 +23,8 @@ env {
//chr_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/reference_genomes/human hg19_grch37/hg19_grch37p5_chr_size_cumul.txt" // human chromo infos
region = "none" // region to parse. Write "chr7:0-147000000, chr10:1000000-2000000" for a single region, "chr7:0-147000000, chr10:1000000-2000000" if two regions, ""chr7" for a whole chromosome, "chr7, chr1" for two chromosomes and "none" for the complete genome // Warning : replace eval() by ast.literal_eval() from ast package in the main py code ?
tsv_extra_fields = "AC AF CSQ_SIFT CSQ_PolyPhen" // subfields from INFO to add as columns in the tsv file. Example: tsv_extra_fields = "AC AF". Write "CSQ_PolyPhen" for a sub field of the CSQ field of INFO. Write "NULL" if not required
- x_lim = "NULL" // x-axis limits. Either "whole" for the whole genome, "region" to have the regions of the region parameter (i.e., "whole" if region == "none"), or a character string written like the region parameter, to have the x-axis limited to the x_lim parameter. Write "NULL" to does not plot results
- bottom_y_column = "AF" // any of the OR, P_VALUE, NEG_LOG10_P_VALUE or PATIENT_NB column of the res.tsv file for the y-axis of the bottom manhattan plot -> miami plot. Can also be an added column through the tsv_extra_fields parameter. Indicated column of field must be quantitative. Write "NULL" to get the res.tsv file and explore the columns before rerunning the nextflow process using - resume. "NULL" generates a simple manhattan plot
+ x_lim = "chr1" // x-axis limits. Either "whole" for the whole genome, "region" to have the regions of the region parameter (i.e., "whole" if region == "none"), or a character string written like the region parameter, to have the x-axis limited to the x_lim parameter. Write "NULL" to does not plot results
+ bottom_y_column = "NULL" // any of the OR, P_VALUE, NEG_LOG10_P_VALUE or PATIENT_NB column of the res.tsv file for the y-axis of the bottom manhattan plot -> miami plot. Can also be an added column through the tsv_extra_fields parameter. Indicated column of field must be quantitative. Write "NULL" to get the res.tsv file and explore the columns before rerunning the nextflow process using - resume. "NULL" generates a simple manhattan plot
color_column = "AF" // as for bottom_y_column in order color the dots. Write "NULL" if not required (dots will be alternatively grey and blue, according to chromo order)
y_lim1 = 3 // max y-axis limit of the top panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Write "NULL" for no particular limit
y_lim2 = 2 // max y-axis limit of the bottom panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Not considered if bottom_y_column = "NULL"
diff --git a/fisher_for_vcf.nf b/fisher_for_vcf.nf
index 1d50077..e82b19b 100644
--- a/fisher_for_vcf.nf
+++ b/fisher_for_vcf.nf
@@ -41,6 +41,8 @@ sample_path_test = file("${sample_path}") // to test if exist below
tbi_path_test = file("${sample_path}.tbi") // to test if exist below
ped_path_test = file("${ped_path}") // to test if exist below
chr_path_test = file("${chr_path}") // to test if exist below
+cute_path_test = file("${cute_path}") // to test if exist below
+out_path_test = file("${out_path}") // to test if exist below
//////// end Variables from config.file that need to be modified
@@ -84,27 +86,59 @@ if(x_lim == 'whole' || (x_lim == 'region' && region == 'none')){ // for the miam
//////// Checks
-if(system_exec == 'local' || system_exec == 'slurm'){
- def file_exists1 = sample_path_test.exists()
- if( ! file_exists1){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID sample_path PARAMETER IN nextflow.config FILE: ${sample_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
- }else if(sample_path_test =~ /.*\.gz$/){
- def file_exists2 = tbi_path_test.exists()
- if( ! file_exists2){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID .tbi FILE ASSOCIATED TO sample_path PARAMETER IN nextflow.config FILE: ${sample_path}.tbi\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\nOTHERWISE, USE tabix -p vcf <NAME>.vcf TO INDEX THE .gz FILE\n\n========\n\n"
- }
- }
- def file_exists3 = ped_path_test.exists()
- if( ! file_exists3){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID ped_path PARAMETER IN nextflow.config FILE: ${ped_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
- }
- def file_exists4 = ped_path_test.exists()
- if( ! file_exists4){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID chr_path PARAMETER IN nextflow.config FILE: ${chr_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
+
+def file_exists1 = sample_path_test.exists()
+if( ! file_exists1){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID sample_path PARAMETER IN nextflow.config FILE: ${sample_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
+}else if(sample_path_test =~ /.*\.gz$/){
+ def file_exists2 = tbi_path_test.exists()
+ if( ! file_exists2){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID .tbi FILE ASSOCIATED TO sample_path PARAMETER IN nextflow.config FILE: ${sample_path}.tbi\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\nOTHERWISE, USE tabix -p vcf <NAME>.vcf TO INDEX THE .gz FILE\n\n========\n\n"
}
-}else{
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID system_exec PARAMETER IN nextflow.config FILE: ${system_exec}\n\n========\n\n"
}
+def file_exists3 = ped_path_test.exists()
+if( ! file_exists3){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID ped_path PARAMETER IN nextflow.config FILE: ${ped_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
+}
+def file_exists4 = chr_path_test.exists()
+if( ! file_exists4){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID chr_path PARAMETER IN nextflow.config FILE: ${chr_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
+}
+
+if( ! region in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID region PARAMETER IN nextflow.config FILE:\n${region}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+}
+if( ! tsv_extra_fields in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID tsv_extra_fields PARAMETER IN nextflow.config FILE:\n${tsv_extra_fields}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+}
+if( ! x_lim in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID x_lim PARAMETER IN nextflow.config FILE:\n${x_lim}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+}
+if( ! bottom_y_column in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID bottom_y_column PARAMETER IN nextflow.config FILE:\n${bottom_y_column}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+}
+if( ! color_column in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID color_column PARAMETER IN nextflow.config FILE:\n${color_column}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+}
+if( ! y_lim1 in Integer ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_lim1 PARAMETER IN nextflow.config FILE:\n${y_lim1}\nMUST BE A SINGLE INTEGER\n\n========\n\n"
+}
+if( ! y_lim2 in Integer ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_lim2 PARAMETER IN nextflow.config FILE:\n${y_lim2}\nMUST BE A SINGLE INTEGER\n\n========\n\n"
+}
+def file_exists5 = cute_path_test.exists()
+if( ! file_exists5){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID cute_path PARAMETER IN nextflow.config FILE:\n${cute_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
+}
+
+if( ! (system_exec == 'local' || system_exec == 'slurm')){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID system_exec PARAMETER IN nextflow.config FILE:\n${system_exec}\n\n========\n\n"
+}
+def file_exists6 = out_path_test.exists()
+if( ! file_exists6){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID out_path PARAMETER IN nextflow.config FILE:\n${out_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
+}
+
//////// end Checks
--
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