Yes, in both cases callRate is the proportion of calls that are non-missing. For variants, it’s measured per row. For samples, it’s measured per column.
Thanks, and I found the minor allele frequency from the variant.qc.AF metrics doesn’t center around 0 (homozygous) and 0.5 (heterozygous) as I expected, any explanation?
Sorry I wasn’t clear about my question: how’s the va.qc.AF field defined. Say we have a total of 3 samples. 1 sample is 0/0, 1 sample is 0/1, and 1 sample is 1/1. is the AF = 0.5 (3 alt alleles /6 possible alleles) or 2/3 (2 out of the 3 samples genotypes being called? Thanks.