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?