Linkage disequilibrium with 1000 Genomes/HapMap

Question

[enricoferrero]

Hi,

I have a set of SNPs associated with a specific trait and I would like to know to what other SNPs, in the 1000 Genomes or HapMap projects, they are in linkage disequilibrium (LD) with.

Is there anything in Bioconductor (or CRAN) that can help me answer this question? I'm basically looking for something like SNAP Pairwise LD from the Broad Institute.

Thanks!

Answer 1

[Mo Sander]

I think you should be able to use the package PLINK/SEQ for that, see also https://atgu.mgh.harvard.edu/plinkseq/tutorial.shtml

Sorry, I just saw that the R package is not available at the moment https://atgu.mgh.harvard.edu/plinkseq/download.shtml ...