Question: Precalculated Ld Blocks
3
gravatar for Radhouane Aniba
7.8 years ago by
Radhouane Aniba750 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.

Cheers

Rad

linkage population snp • 2.4k views
ADD COMMENTlink modified 7.7 years ago by Larry_Parnell16k • written 7.8 years ago by Radhouane Aniba750
5
gravatar for Pierre Lindenbaum
7.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum117k wrote:

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

ADD COMMENTlink written 7.8 years ago by Pierre Lindenbaum117k

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

ADD REPLYlink written 2.6 years ago by cmdcolin1.1k
2
gravatar for Khader Shameer
7.7 years ago by
Manhattan, NY
Khader Shameer18k wrote:

LocusZoom is another program with similar capabilities.

You can also try Haploview.

ADD COMMENTlink written 7.7 years ago by Khader Shameer18k
0
gravatar for Larry_Parnell
7.8 years ago by
Larry_Parnell16k
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 7.7 years ago • written 7.8 years ago by Larry_Parnell16k
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