Tagsnps: Is There A Tool To Select Tagsnps That Tag Exons?

Question

[Valerie]

Hello, I am looking for a tool/way to select tagSNPs efficiently. I would like to have Exons + Promoter covered. However the amount of SNPs I can include in my panels is limited and I would like to use CEU + YRI pop. Does someone would have an easy way/tool to do so? I have already tried with Tagger but it is using dbSNP126, which is pretty old... thanks!

Answer 1

[Larry_Parnell]

Unfortunately, I know of no such tool to accomplish your desired tasks. I use SNAP at the Broad. This gives you the proxy SNPs along with genome coordinates, which you can then cross-check against exon and promoter coords to label each proxy as belong to or outside exons. When I run SNAP, I set it to 1000 Genomes Pilot 1 data, much more up to date.

Answer 2

[Yahan]

You could have a look at HapBlock.

It calculates haplotype blocks using different user defined criteria.

Tagsnps can also be calculated with different linkage criteria, and it outputs all the possible tagsnp for each block.

You can also specify the maximum size of the blocks.

So if you only use snps within promoters or exons, that should approximate what you want to do.

But there is no automated retrieval from NCBI or so, so you'd have to format your input data yourself, but the format is pretty straightforward.