I am wondering if anyone knew whether the UKB WES VCFs contain homozygous reference positions? To be specific, the positions where all samples are 0/0.
It is VCF of the 200K Exome OQFE variant call files (VCFs) that I'm working with. The documentation and supplemental materials of publications refer to these VCFs as gVCF. However, it is unclear by looking into the VCF, whether the missing positions are omitted because they are homozygous reference.
Any answer will be much appreciated.