I want to get allele frequencies of Illumina Omni2.5 in European population only and my file contains information on chr, pos, allele1, and allele2. I though there could be two ways of doing it:
1. Annotate Reference and Alternate allele for each SNP (how??) and use Annovar to get 1000 genome population specific allele frequency
2. Download allele frequency information from HapMap/1000 Genome directly.
Does any one has any good suggestions on how to go about it or recommend any software?
Thanks in advance!