Question: Report haplotype frequencies from a region within a phased vcf file
gravatar for Krisr
3.5 years ago by
United States
Krisr460 wrote:


I am interested in obtaining haplotypes (and their frequencies) from a region of the human genome from a particular population from the Phase3 1000 genomes data. I have downloaded the corresponding chromosome ( and used tabix and VCF tools to obtain the genotype data for the region of interest from a subset of of subjects corresponding to CEU. Does anyone know of a workflow to utilize data of this sort to infer haplotypes and their frequencies across the region specified in the subsetted VCF?


snp haplotype variation • 1.8k views
ADD COMMENTlink modified 23 months ago by Biostar ♦♦ 20 • written 3.5 years ago by Krisr460

Does this prior post help you: Haplotype frequencies from 1000 genomes

ADD REPLYlink written 3.5 years ago by Vincent Laufer1.1k

Thanks for the reply, it is a solution I may try. I was wondering if there was a workflow using pre-existing tools already coded and available.

ADD REPLYlink written 3.5 years ago by Krisr460

Not that I see from a quick search of the net, but you are right to post it on a blog like this cause people have almost certainly done it.

I would: 1) download 1kg phased VCF file 2) trim to just the SNPs I wanted 3) convert into my desired input format for Haploview ( 4) offload haplotype frequency calculation to haploview (easy to code, but this gives you everything else in the GUI).

ADD REPLYlink written 3.5 years ago by Vincent Laufer1.1k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1717 users visited in the last hour