to try and add some population frequency info to a set of ~40K variants. We are interested in NFE (non-Finnish European) ancestry but there are about 30 different flavors of this (male, female, nfe_nwe, nfe_onf, non_topmed_nhomalt_non-neuro nfe etc.) I can’t seem to find a field that reflects the general nfe population. Unfortunately we need to work on the hg19 coordinates, so the file is the hg19 exomes (which I don’t see on the website anymore).
Can someone suggest which is best and likely to have the most alleles?
If you’re interested in the NFE genetic ancestry group as a whole (not split by subset or inferred sex), you should look at whichever metric you are interested in, followed by only “_nfe”. For example:
##INFO=<ID=AC_nfe,Number=A,Type=Integer,Description=“Alternate allele count for samples of Non-Finnish European ancestry”>
##INFO=<ID=AN_nfe,Number=1,Type=Integer,Description=“Total number of alleles in samples of Non-Finnish European ancestry”>
##INFO=<ID=AF_nfe,Number=A,Type=Float,Description=“Alternate allele frequency in samples of Non-Finnish European ancestry”>
