Question: Non-overlapping genomic haplotype blocks
0
gravatar for avinash.sahu
4.1 years ago by
avinash.sahu10
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 • 2.0k views
ADD COMMENTlink modified 2.9 years ago by bmpbowen40 • written 4.1 years ago by avinash.sahu10
0
gravatar for bmpbowen
2.9 years ago by
bmpbowen40
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. 

 

http://bioinformatics.oxfordjournals.org/content/early/2015/10/01/bioinformatics.btv546

ADD COMMENTlink written 2.9 years ago by bmpbowen40
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