Question: Non-overlapping genomic haplotype blocks
gravatar for avinash.sahu
6.5 years ago by
United States
avinash.sahu10 wrote:

Hi All,


I am trying to search list of non-overlapping haplotype blocks for CEU population (or based on 1000Genome project). I searched Hapmap and 1000 Genome database they have Phased haplotypes but not genomic-cordinates of the Haplotype blocks.

Do I have to download Genotype data and run plink to get haplotype blocks coordinates. That's look time-consuming because plink is slow for finding haplotypes ( I tried with 313 genotype and plink have only finished 60 Mb in 5 hours for finding haplotype blocks).

tool ld haplotye 1000 genome hapmap • 2.8k views
ADD COMMENTlink modified 5.3 years ago by bmpbowen40 • written 6.5 years ago by avinash.sahu10
gravatar for bmpbowen
5.3 years ago by
United States
bmpbowen40 wrote:

This might be helpful: "Approximately independent linkage disequilibrium blocks in human populations" by Berisa and Pickrell. They released LD blocks for AFR, ASN, and CEU populations using 1000 genomes data.

ADD COMMENTlink written 5.3 years ago by bmpbowen40
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