Question

Precalculated Ld Blocks

3

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12.8 years ago

Radhouane Aniba ▴ 790

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 • 4.1k views

ADD COMMENT • link updated 12.8 years ago by Larry_Parnell 16k • written 12.8 years ago by Radhouane Aniba ▴ 790

score 5 · Answer 1 · 2011-06-15

5

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12.8 years ago

Pierre Lindenbaum 161k

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

ADD COMMENT • link 12.8 years ago by Pierre Lindenbaum 161k

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

ADD REPLY • link 7.7 years ago by cmdcolin ★ 3.8k

score 2 · Answer 2 · 2011-06-30

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12.8 years ago

Khader Shameer 18k

LocusZoom is another program with similar capabilities.

You can also try Haploview.

ADD COMMENT • link 12.8 years ago by Khader Shameer 18k

score 0 · Answer 3 · 2011-06-15

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12.8 years ago

Larry_Parnell 16k

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 COMMENT • link 12.8 years ago by Larry_Parnell 16k