Commit a65d314e authored by hjulienne's avatar hjulienne

add scripts

parent 7327b8a9
......@@ -79,14 +79,14 @@ RAISS has an interface with the command line (see Command Line Usage bellow).
If you have access to a cluster, an efficient way to use RAISS is to launch
the imputation of each chromosome on a separate cluster node. The script
`launch_imputation_all_gwas.sh <https://gitlab.pasteur.fr/statistical-genetics/raiss/blob/master/launch_imputation_all_gwas.sh>`_
`launch_imputation_all_gwas.sh <https://gitlab.pasteur.fr/statistical-genetics/raiss/blob/master/scripts/launch_imputation_all_gwas.sh>`_
contain an example of raiss usage with a SLURM scheduler.
Output
======
The raiss package outputs imputed GWAS files in the tabular format:
#TODO suppress complementary columns
..TODO suppress complementary columns
+------------+---+--+----------------+-----+-----+----------------+------------------+---------+---------+
| |A0 |A1| Nsnp_to_impute |Var |Z |condition_number|correct_inversion |ld_score | pos |
......@@ -94,7 +94,6 @@ The raiss package outputs imputed GWAS files in the tabular format:
| rs11584349 |C | T| 18 | 0.85|-0.28| 116.9 | False | 1.34 | 1000156 |
+------------+---+--+----------------+-----+-----+----------------+------------------+---------+---------+
# Keep only useful columns
Command Line Usage
==================
......
GIANT_HEIGHT chr1
GIANT_HEIGHT chr2
GIANT_HEIGHT chr3
GIANT_HEIGHT chr4
GIANT_HEIGHT chr5
GIANT_HEIGHT chr6
GIANT_HEIGHT chr7
GIANT_HEIGHT chr8
GIANT_HEIGHT chr9
GIANT_HEIGHT chr10
GIANT_HEIGHT chr11
GIANT_HEIGHT chr12
GIANT_HEIGHT chr13
GIANT_HEIGHT chr14
GIANT_HEIGHT chr15
GIANT_HEIGHT chr16
GIANT_HEIGHT chr17
GIANT_HEIGHT chr18
GIANT_HEIGHT chr19
GIANT_HEIGHT chr20
GIANT_HEIGHT chr21
GIANT_HEIGHT chr22
GIANT_BMI chr1
GIANT_BMI chr2
GIANT_BMI chr3
GIANT_BMI chr4
GIANT_BMI chr5
GIANT_BMI chr6
GIANT_BMI chr7
GIANT_BMI chr8
GIANT_BMI chr9
GIANT_BMI chr10
GIANT_BMI chr11
GIANT_BMI chr12
GIANT_BMI chr13
GIANT_BMI chr14
GIANT_BMI chr15
GIANT_BMI chr16
GIANT_BMI chr17
GIANT_BMI chr18
GIANT_BMI chr19
GIANT_BMI chr20
GIANT_BMI chr21
GIANT_BMI chr22
#!/bin/bash
#SBATCH --mem=32000
#SBATCH -o /pasteur/projets/policy01/PCMA/WKD_Hanna/impute_for_jass/genome_imputation_script/imputation_log/IMPFJ_%a.log
#SBATCH -e /pasteur/projets/policy01/PCMA/WKD_Hanna/impute_for_jass/genome_imputation_script/error_log/error_%a.log
#define data location
module load Python/3.6.0
output_folder="/pasteur/projets/policy01/PCMA/1._DATA/ImFJ_imputed_zfiles"
ref_folder="/pasteur/projets/policy01/PCMA/1._DATA/ImpG_refpanel"
zscore_folder="/pasteur/projets/policy01/PCMA/1._DATA/ImpG_zfiles"
ld_folder="/pasteur/projets/policy01/PCMA/WKD_Hanna/impute_for_jass/berisa_ld_block"
args=$(head -n ${SLURM_ARRAY_TASK_ID} $1 | tail -n 1)
study=$(echo $args | cut -d' ' -f1)
chrom=$(echo $args | cut -d' ' -f2)
#quick fix to access entry point on tars
alias impute_jass="python3 /pasteur/homes/hjulienn/.local/lib/python3.6/site-packages/impute_jass/__main__.py"
#study="GIANT_HEIGHT"
#chrom="chr22"
echo "Study: ${study}; Chrom: ${chrom}"
#time impute_jass --chrom ${chrom} --gwas ${study} --ref-folder ${ref_folder} --ld-folder ${ld_folder} --zscore-folder ${zscore_folder} --output-folder ${output_folder}
time python3 /pasteur/homes/hjulienn/.local/lib/python3.6/site-packages/impute_jass/__main__.py --chrom ${chrom} --gwas ${study} --ref-folder ${ref_folder} --ld-folder ${ld_folder} --zscore-folder ${zscore_folder} --output-folder ${output_folder}
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