Plink --het function and sample size

Question

[cge]

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.

[cge]

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).

[krishii]

How did you over come this problem?? I am also facing the same problem

Answer 1

[chrchang523]

--het requires fairly accurate allele frequencies. If you are not using --read-freq, results will depend on the allele frequencies in your immediate dataset, and will be wildly inaccurate if your dataset has few samples.