Entering edit mode
2.6 years ago
anamaria ▴ 180
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?
Did you ever find the answer to this @anamaria? I am trying to do this currently - thanks
Sorry to be the bearer of bad news, but if you're looking for "individual-level allele frequencies" on a genotype callset, you're almost certainly doing something wrong. Do you know what are the possible individual-level allele frequency values?