From 845dfd26a185a82e04388df0e50227b078e29656 Mon Sep 17 00:00:00 2001
From: hanna julienne <hanna.julienne@pasteur.fr>
Date: Wed, 30 Oct 2019 12:02:09 +0100
Subject: [PATCH] filter ambiguous SNPs

---
 jass_preprocessing/map_reference.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/jass_preprocessing/map_reference.py b/jass_preprocessing/map_reference.py
index 1b0f395..c630149 100644
--- a/jass_preprocessing/map_reference.py
+++ b/jass_preprocessing/map_reference.py
@@ -23,6 +23,9 @@ def read_reference(gwas_reference_panel, mask_MHC=False, minimum_MAF=None, regio
     ref = pd.read_csv(gwas_reference_panel, header=None, sep= "\t",
                       names =['chr', "pos", "snp_id", "ref", "alt", "MAF"],
                        index_col="snp_id")
+    #Filter Strand ambiguous
+    ref = ref.loc[~(ref.ref+ref.alt).isin(["AT", "TA", 'CG','GC'])]
+
     if mask_MHC:
         ref = ref.loc[(ref.chr !=6)|(ref.pos < 28477797)|(ref.pos > 33448354)]
 
-- 
GitLab