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Precalculated Ld Blocks

Hi everyone,

I have a list of SNPs and would like to search for proxy SNPs in LD blocks under some thresold of r2 and distance, I found SNAP which is a good tool but I would like to see if someone have used / know another tool for that.

Cheers

Rad

snp linkage population
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updated by Larry_Parnell Larry_Parnell • written by Radhouane Aniba Radhouane Aniba

3 answers

the Hapmap LD data are available for download: http://hapmap.ncbi.nlm.nih.gov/downloads/ld_data/latest/

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written by Pierre Lindenbaum Pierre Lindenbaum

LocusZoom is another program with similar capabilities.

You can also try Haploview.

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written by Khader Shameer Khader Shameer

We use both SNAP and the HapMap data extensively. Right now, we prefer SNAP because it uses phase I data from the 1000 Genomes Project. Remember, one goal of 1000G was to build a catalog of human genetic variation - so this is very important data to use.

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written by Larry_Parnell Larry_Parnell

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