Question: Haplotype Frequency Calculator For Vcf Files
gravatar for diviya.smith
6.7 years ago by
United States
diviya.smith50 wrote:

Aim: Download public data in a range, calculate the haplotype frequency for SNPs in the region for each ethnic population.

I want to compute haplotype frequencies for several markers in a region for each 1000 genomes ethnic population. I was wondering if there is any tool like vcftools or other that can be used for this purpose. Specifically, for a set of regions, I want to find the genotypes for all markers in the region and compute the haplotype frequencies.

Right now, I am manually doing this by extracting each region from the vcf file using tabix-

    tabix -h 17:1471000-1472000 | vcf-subset -c CEU.list >CEU_region1.vcf

And then computing the frequency of every haplotype for each pair of SNPs in the region. The regions I am considering are small and typically contain only 2-3 SNPs and most of 1000 genomes data is phased and so this is not too computationally expensive but a little cumbersome.

Can anyone suggest a better solution to this problem?

vcf haplotype • 3.5k views
ADD COMMENTlink modified 5.8 years ago by Anne0 • written 6.7 years ago by diviya.smith50
gravatar for Anne
5.8 years ago by
United States
Anne0 wrote:

Hi Diviya,

I am having the exact same question, so if by any chance you managed to find a good solution it would be great if you could let me know!





ADD COMMENTlink written 5.8 years ago by Anne0
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