Hardy Weinberg data from 1000 genomes project
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7.0 years ago
sp16027 • 0

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

SNP genome • 1.9k views
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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

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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.

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

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7.0 years ago
Vivek ★ 2.7k

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
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How do I select specific populations using the code provided?

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