filter ambiguous SNPs

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)]