Hardy Weinberg data from 1000 genomes project
1 answer
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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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
Please use
ADD COMMENTorADD REPLYto 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.Why would you not use plink? It's like the swiss army knife of all statistical variant analysis.