Could anyone show me a straightforward method to retrieve genotypic frequencies from a
I mean, not the expected frequencies calculated assuming Hardy Weinberg equilibrium from the allelic frequencies, but the real genotypic frequencies.
I found a way using
--hardy option, which gives you the genotype counts, amongst many other stuff, and from these counts retrieve the frequencies. But I was wondering if a more simple way, analog the
--freq option from plink or
vcftools for the allelic frequencies. I know this may be a silly question, but had not found anything.
Thanks in advance,