Alternative to SNAP (Broad) for finding SNPs in LD to initial set?

[albireo]

Hi

I have a list of SNPs and would like to recover all SNPs in strong LD with them (let's say 0.9) within a population (for example CEPH).

There is a web interface which does this (SNAP by broad) however this is quite old and only works with LD data from hapmap and 1000genomes pilot 1 data.

Are you aware of any other similar resource able to use more recent 1000g data?

Any suggestions are greatly appreciated.

[chrisedlund]

Try rAggr (http://raggr.usc.edu/), which has the most recent version of 1000 Genomes (Phase 3).

Here's a description:

rAggr finds proxy markers (SNPs and indels) that are in linkage-disequilibrium (LD) with a set of queried markers, using the 1000 Genomes Project and HapMap genotype databases. rAggr uses an expectation–maximization algorithm adapted from the Haploview software (Barrett et al., 2005) to calculate pairwise r2 and D'.