Hardy Weinberg data from 1000 genomes project

Question

[sp16027]

Good morning,

Can anyone advise on how to access Hardy Weinberg data for specific SNPs from the 1000 genomes project? I would like to compare my own HW data to that of larger studies. Many thanks for your help

Best wishes,

Silvia

[sp16027]

Dear Vivek, thank you kindly for your reply. Is there a way to browse the data for a few selected SNPs without using PLINK? Many thanks

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

[WouterDeCoster]

Why would you not use plink? It's like the swiss army knife of all statistical variant analysis.

Answer 1

[Vivek]

It should be relatively straightforward to calculate using something like this:

You can get the SNPs for your region of interest using Tabix:

tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz 2:39967768-39967768 > extracted.vcf

Use PLINK to convert to binary ped

plink --vcf extracted.vcf --make-bed --out extracted

Calculate HWE p-values using PLINK:

plink --bfile extracted --hardy --out extracted-hwe

[sp16027]

How do I select specific populations using the code provided?