I have a set of patient VCF files, and I am looking at the genotypes of each variant called. I observe the three expected categories:
0/0 : homozygous for the reference allele 0/1 : heterozygous (one ref allele, one alt allele) 1/1: homozygous for the alternate allele
My question is, what is the point of calling a homozygous reference allele? Is this only done when there is low confidence on the variant call? To as to say "hey, this could be a different genotype, but here's what we got with the data quality given"?
What would I lose if I filtered all rows in my VCFs out with the genotype listed as "0/0"?