I am trying to find the minor allele frequency of all of the SNPs and INDELs from the 1000Genomes EUR reference.
It was taking too long to compute the frequencies of ALL the variants using vcftools as outlined here Getting Allele Frequencies From 1000 Genomes, so I tried extracting the allele frequency reported in the vcf files under the "EUR_AF" to get a list for each variant of: chromosome, position, EUR_AF, however I don't think this is the minor allele frequency.
The vcf file reports:
##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN"
with the AC being the "Alternate Allele Count" and AN the "Total Allele Count".
Would I need to also extract the AC and AN columns (and also maybe the AA, i.e. "ancestral allele"?) to derive which allele the vcf is referring to, or does anyone know of a better way to do this?
Thank you for any suggestions!