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Posts by scrap
... I think it is because `nhomalt` is the number of individuals homozygous for the *alternate allele*. `AN/2` = total number of individuals, but that includes individuals homozygous for the reference allele, heterozygotes, and individuals homozygous for the alternate allele (`nhomalt`). So, `AN/2 - nh ...
... For non-sex chromosome (and female Y chrom) variants I think the correct calculation for number of heterozygous individuals would be `AC - (2 x nhomalt)`. Each homozygous individual contributes 2 alternate alleles to the allele count (AC), so all remaining AC must come from heterozygous individuals ...
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