Getting Population Specific Allele Frequency For Illumina Genotyping Data

Question

[yling1]

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!

[Katie D'Aco]

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)

[Danielson]

@Katie D'Aco Then what would you use?

[Katie D'Aco]

I think 1000 genomes frequencies would be fine to use here.

[Danielson]

I though the HapMap frequencies were deduced from the 1000genomes project. I hoped new projects, such as kaviar, would supersede the original 1000genomes.

Answer 1

[Charles Warden]

SeattleSNP can use a "custom" file format that will accept the FinalReport allele calls with a bit of reformatting (remove rows without allele calls):

http://snp.gs.washington.edu/SeattleSeqAnnotation138/

It will provide the reference sequence as well as specifically provide the European HapMap frequency.

That said, be careful how you export your data. I think the default in GenomeStudio is to use the "TOP" format. However, this often won't match the genomic reference. Once you know the built for which the genome coordinates are defined (e.g. hg18 or hg19), you should use the "Plus" format to get the alleles with respect to that reference. If you can only get hg18 coordinates, you'll need to use liftOver (in Galaxy, etc.) to convert them to hg19.