I'm using GATK version 184.108.40.206 with a command that looks like
gatk VariantsToTable -V file.vcf -O file.tsv -F CHROM -F POS -F TYPE -F REF -F ALT -GF AD -GF GT -F DP -F QUAL -F ANN
Is there any way to output numeric genotypes (as they are in the VCF) when using VariantsToTable?
For example, I'd rather just see 0/1 than CTACCCT/AACCCA in the resulting tsv, since that info is already in the REF and ALT fields, and I have quite a lot of samples that each have their own genotype. But it seems that VariantsToTable automatically converts the numeric genotypes to the actual bases. I can see why that behavior would be desirable sometimes, but is there any way to turn it off? I've read through the options and couldn't find one. Thanks!
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