It converts a haploid genotype 0 or 1 to a dot; for example:
GT:DP:GQ:MIN_DP:PL 0:53:99:18:0,666 to .:53:99:18:0,666
IIRC, this is intended behavior, and happens with any ploidy. GVCFs are not intended to be used as final calls, and GGVCFs doesn't use the genotype field
Thanks for the quick response! I'm going to feed the combined gvcf file to GenotypeGVCFs. If GenotypeGVCFs does not use the GT field, what field is used?
PL. It's all likelihood-based, which is where the benefit of joint calling over naive conglomeration comes in
I see, thanks a bunch! @pdexheimer