Entering edit mode
3.4 years ago
nhaus
▴
300
Hello everybody,
I am currently working with a one sample VCF file and a lot of my variants have 0/0 in their GT field, which means that they are homozygous for the ref base at that position if I am not mistake. If this is the case, I am wondering why they are even recorded in the VCF file in the first place, since they are not a variant.
If someone could point out what the benefit of including these "variants" in the VCF file is, I would be very grateful.
Was this VCF generated by a variant caller directly or was it obtained by splitting a multi-sample VCF? As in, is there a possibility some sort of manipulation done after variant callling could have introduced this?
I unfortunately do not know this. But this could be an explanation. If it was a multisample vcf file that was split, then the GT 0/0 would make sense. Thanks!