We have several thousand GWAS SNPs which are significantly associated with disease in two populations (CHB and a Korean population). We want to select tag SNPs to genotype in a followup sample. If there are several SNPs which tag a set of significant SNPs, we want to choose the one that has the best P-value. NIEHS has a tool which can do this for candidate genes http://snpinfo.niehs.nih.gov/selegene.htm and it also has one which does functional SNPs http://snpinfo.niehs.nih.gov/selegwas.htm using P-value priorities. I'm certain this tool is out there. But we want something that will select tag SNPs using Hapmap LD like these tools for the whole genome. Forgive me if I'm overlooking the obvious.
We have a little script that does this but it constantly requires re-formatting the data and giving it new LD data, so it would be nice to have a permanent solution to this which could use a simple format like the GWAS-P format on the sites mentioned above.