Hi, I would like to use the latest 1000 genomes project to pick tag SNPs for a genetic association study. Is there an efficient and quick way to do this? Are there any tutorials or software that make the task of picking tagSNPs from the 1000 genomes project easier? Thanks for your time!
To get proxy SNPs, r^2, Dprime etc. You can have a look at the following link from BROAD (1000G is included):
all the best Thomas
ArielSonique asked: How do you decide which of the 0.8 LD SNPs to then pick?
I usually don't because it can be a lot of computational work to decide the putative function of each SNP and to then prioritize all those proxy SNPs to the one (maybe two) that you'll genotype. Search for this topic on BioStar as it has been asked before and many great answers were provided. Try this question, for example.
That said, I'd let the genotyping data I have - say from GWAS - tell me which SNPs already have genotyping data. Or, we would use data from the genotyping assay provider tell us which SNP(s) to genotype because they had the assay for sale (as opposed to designing a new assay for another SNP).
Tagger by the Broad Institute.
Web-based interface, sends you a link via email once it's done.