Converting GP field in a VCF to GT
My VCF file is only populated with posterior genotype probabilities (GP - derived from a BGEN file) 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
1 answer
After abit more digging around, I found the following solution:
QCTool
qctool -g input.vcf.gz -threshold 0.9 -og output.gt.vcf.gz
https://www.well.ox.ac.uk/~gav/qctool_v2/documentation/examples/converting_genotypes.html
"the output VCF file will contain two FORMAT fields, namely GT (the threshholded call) and GP (the original imputed probabilities)".
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