Hi there,

Could anyone show me a straightforward method to retrieve genotypic frequencies from a `tped`

or `vcf`

?

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 `plink`

's `--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,

P.

I don't understand the problem, please clarify. As

`--freq`

with`--counts`

would give you counts? Also, try`--model`

option, it gives all sorts of counts, too.I think it is clear enough... It is simply (to) "retrieve genotypic frequencies from a tped or vcf". Not genotype counts, but frequency numbers directly. I was just wondering if there was a method to retrieve it in the same format as when you retrieve the allele frequencies with vcftools or plink. That's all...