Comparing top SNPs in GWAS

Question

[Varun]

Hello,

I have the summary data from two genome wide association studies of related traits. I want to compare the two gwas, to find if there is an enrichment of SNPs below a certain P-value form GWAS 1 in GWAS 2. Does anyone know of any software or paper to go about this? I get the feeling that I'm looking for a hypergeometric test of some sort.

Any help will be greatly appreciated.

Thanks,
V

[A. Blizzard]

Hi there, did you ever find a way to compare (or assess the difference) two sets of GWAS p-values?