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Plink --het function and sample size

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.

snp
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updated by krishii • krishii • written by cge • 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).

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written by cge • cge

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

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written by krishii • krishii

1 answer

--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.

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written by chrchang523 chrchang523

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