Question: Precalculated Ld Blocks
3
gravatar for Radhouane Aniba
8.3 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 • 2.6k views
ADD COMMENTlink modified 8.2 years ago by Larry_Parnell16k • written 8.3 years ago by Radhouane Aniba750
5
gravatar for Pierre Lindenbaum
8.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum122k wrote:

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

ADD COMMENTlink written 8.3 years ago by Pierre Lindenbaum122k

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

ADD REPLYlink written 3.1 years ago by cmdcolin1.2k
2
gravatar for Khader Shameer
8.2 years ago by
Manhattan, NY
Khader Shameer18k wrote:

LocusZoom is another program with similar capabilities.

You can also try Haploview.

ADD COMMENTlink written 8.2 years ago by Khader Shameer18k
0
gravatar for Larry_Parnell
8.3 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 8.2 years ago • written 8.3 years ago by Larry_Parnell16k
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