Allelotyping - Pooled Dna With Illumina Omniexpress

Question

[1234Jc4321]

Has anyone ever had to analyze genome wide genotypes from pooled DNA using the Illumina OmniExpress chip.

I know there are several approaches. However, none of them works for me. SNPMap only works for the Affymetrix chips, and GPFrontend GPGraphics too. UPDG was also a possibility but I think that this package requires individual genotyping data to work while I have only the genotypes for the pooled DNA.

Does anyone knows another solution that could handle this?

thanks

Answer 1

[Wen.Huang]

I've done this before and I wrote my own code to do Z test to compare allele frequencies. Look up this paper: Am J Hum Genet, Jan;80(1):126-39. 2007 by Pearson et al. I think they also publish some code you may be able to use.