Question: Haplotype Block Database
2
gravatar for Nathan Harmston
8.6 years ago by
Nathan Harmston1.1k
London
Nathan Harmston1.1k wrote:

Hi,

I'm trying to find a database of precomputed haplotype blocks (really interested in just the CEU population or cell line GM12878). However searching around doesn't seem to provide me with anything.

I obviously have access to the HapMap LD data and I am trying to associate haplotype blocks with a list of SNPs I have ( trying to see if there is anything interesting within then). Do most people download the hapmap data and then process it themselves using haploview / plink etc ? This seems a little wasteful. I had assumed that there would be a precomputed set of blocks somewhere to download and just use.

Thanks

hapmap database haplotype • 5.7k views
ADD COMMENTlink modified 7.9 years ago by scottwilliamrobinson130 • written 8.6 years ago by Nathan Harmston1.1k
1
gravatar for tiagoantao
8.6 years ago by
tiagoantao670
United States of America
tiagoantao670 wrote:

HapMap also has phased data, not only LD, check:

ftp://ftp.hapmap.org/hapmap/phasing/2009-02_phaseIII/HapMap3_r2/

ADD COMMENTlink written 8.6 years ago by tiagoantao670
1
gravatar for mrxcm3
8.6 years ago by
mrxcm350
mrxcm350 wrote:

Perhaps try the SNAP Proxy Search tool (http://www.broadinstitute.org/mpg/snap/ldsearch.php)?

ADD COMMENTlink written 8.6 years ago by mrxcm350
0
gravatar for scottwilliamrobinson
7.9 years ago by
United Kingdom
scottwilliamrobinson130 wrote:

Try DistiLD, click the mutation tab, enter your 'rs' number then at the following page click submit. I think this is what you are after :)

ADD COMMENTlink written 7.9 years ago by scottwilliamrobinson130
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