Commit 845dfd26 authored by Hanna  JULIENNE's avatar Hanna JULIENNE
Browse files

filter ambiguous SNPs

parent fa601f18
...@@ -23,6 +23,9 @@ def read_reference(gwas_reference_panel, mask_MHC=False, minimum_MAF=None, regio ...@@ -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", ref = pd.read_csv(gwas_reference_panel, header=None, sep= "\t",
names =['chr', "pos", "snp_id", "ref", "alt", "MAF"], names =['chr', "pos", "snp_id", "ref", "alt", "MAF"],
index_col="snp_id") index_col="snp_id")
#Filter Strand ambiguous
ref = ref.loc[~(ref.ref+ref.alt).isin(["AT", "TA", 'CG','GC'])]
if mask_MHC: if mask_MHC:
ref = ref.loc[(ref.chr !=6)|(ref.pos < 28477797)|(ref.pos > 33448354)] ref = ref.loc[(ref.chr !=6)|(ref.pos < 28477797)|(ref.pos > 33448354)]
......
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