Hello, I am using the --het function in Plink1.9, and I noticed that the results for the number of homozygous genotypes in each individual is dependent by the sample size, with a direct relationship with the sample size. Should not be just the count homozygous/total variants? How the sample size can affect that? I expected that just for the expected heterozygosity, when computed with the Nei's formula.

Thanks, S.

Thank you for your comment, but as far I can read in the manual, --read-freq is just for the expected homozygosity (and it makes sense).