Hello,

I am wondering if there is a paper or a workflow which deals with individual-level allele frequencies.

In plink so far I only see the option to calculate allele frequencies for all individuals (prior doing GWAS): I would first prune SNPs

plink --bfile Merge --max-maf 0.05 --exclude inversion.txt --range --indep-pairwise 50 5 0.2 --out indepSNP

and calculate allele frequencies

plink --bfile Merge --extract indepSNP.prune.in  --freq  --out freq_stat

But how would I find allele frequencies per individual for a set of common pruned SNPs from my plink data?

Thanks