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:
- Annotate Reference and Alternate allele for each SNP (how??) and use Annovar to get 1000 genome population specific allele frequency
- 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!
I wouldn't use HapMap frequencies, since they didn't use the 2.5 chip in their genotyping (according to the genotyping platform filter in HapMart)
@Katie D'Aco Then what would you use?
I think 1000 genomes frequencies would be fine to use here.
I though the HapMap frequencies were deduced from the 1000genomes project. I hoped new projects, such as kaviar, would supersede the original 1000genomes.