Non-overlapping genomic haplotype blocks

Question

[avinash.sahu]

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).

Answer 1

[bmpbowen]

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.