Precalculated Ld Blocks

Question

[Radhouane Aniba]

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

Answer 1

[Pierre Lindenbaum]

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

[cmdcolin]

Downloads now only available through ftp ftp://ftp.ncbi.nlm.nih.gov/hapmap/

Answer 2

[Khader Shameer]

LocusZoom is another program with similar capabilities.

You can also try Haploview.

Answer 3

[Larry_Parnell]

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.