Hello everybody. I have a question regarding the --het PLINK command. PLINk’s manual doesn’t tell us much, just that: “computes observed and expected autosomal homozygous genotype counts for each sample, and reports method-of-moments F coefficient estimates (i.e. ([observed hom. count] - [expected count]) / ([total observations] - [expected count]))”. However this is not indeed the inbreeding coefficient calculated by Fis. First of all because the Fis (or panmictic index) is calculated with the number of observed and expected heterozygosity. Also Fis is a value of the population not of the individual, indeed PLINK give us an inbreeding coefficient per individual. Because all of this, I think that --het in PLINK is not a pure inbreeding coefficient by Fis. But perhaps I’m wrong. Does anybody knows what’s going on with this PLINK’s coefficient?
