Converting GP field in a VCF to GT
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3 days ago
Garan ▴ 680

My VCF file is only populated with posterior genotype probabilities (GP) for each variant, is there any way to convert the GP field to GT (genotyped 0/0, 0/1, 1/1 or ./.)? Could anyone suggest a bit of software which can easily handle 10K odd human samples imputed with HRC v1.1?

#CHROM POS    ID     REF    ALT    QUAL   FILTER INFO   FORMAT 31610M
1      13380  1:13380 C      G      .      .      .      GP     1,0,0

to

#CHROM POS    ID     REF    ALT    QUAL   FILTER INFO   FORMAT 31610M
1      13380  1:13380 C      G      .      .      .      GT:GP     0/0:1,0,0
VCF GT GP • 139 views
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