Question: Hardy Weinberg data from 1000 genomes project
0
gravatar for sp16027
3.3 years ago by
sp160270
sp160270 wrote:

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 • 992 views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by sp160270

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

ADD REPLYlink written 3.3 years ago by sp160270

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.

ADD REPLYlink written 3.3 years ago by WouterDeCoster44k

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

ADD REPLYlink written 3.3 years ago by WouterDeCoster44k
2
gravatar for Vivek
3.3 years ago by
Vivek2.4k
Denmark
Vivek2.4k wrote:

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
ADD COMMENTlink written 3.3 years ago by Vivek2.4k

How do I select specific populations using the code provided?

ADD REPLYlink written 13 months ago by sp160270
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