Question: Precalculated Ld Blocks
gravatar for Radhouane Aniba
8.8 years ago by
Radhouane Aniba760 wrote:

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.



linkage population snp • 2.8k views
ADD COMMENTlink modified 8.7 years ago by Larry_Parnell16k • written 8.8 years ago by Radhouane Aniba760
gravatar for Pierre Lindenbaum
8.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

the Hapmap LD data are available for download:

ADD COMMENTlink written 8.8 years ago by Pierre Lindenbaum127k

Downloads now only available through ftp

ADD REPLYlink written 3.6 years ago by cmdcolin1.3k
gravatar for Khader Shameer
8.8 years ago by
Manhattan, NY
Khader Shameer18k wrote:

LocusZoom is another program with similar capabilities.

You can also try Haploview.

ADD COMMENTlink written 8.8 years ago by Khader Shameer18k
gravatar for Larry_Parnell
8.8 years ago by
Boston, MA USA
Larry_Parnell16k wrote:

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.

ADD COMMENTlink modified 8.8 years ago • written 8.8 years ago by Larry_Parnell16k
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