Plink --het function and sample size
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5.1 years ago
cge • 0

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 • 2.0k views
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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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5.1 years ago

--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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