Question: Computing pair-wise R-squared using PLINK (or other packages)
gravatar for hsinyen9
21 months ago by
hsinyen90 wrote:

For my project, I have a list of target SNPS. For each target SNP, I want to generate a list of SNPs within HapMap that have r^2>0.5 with the given SNP.

I have been trying to do so using Plink:

Originally I tried something like this:

plink --bfile mydata 
          --ld-snp rs12345 
          --ld-window-r2 0.5

However, the r-squared value used in this command is only an estimation (The squared correlation based on genotypic allele counts is therefore not identical to the r-sq as estimated from haplotype frequencies).

Is there a command that is similar to the above, but computes accurate r-squared values? Or is there another program/package that I can use to achieve the task?

Thank you!

snp genome • 961 views
ADD COMMENTlink modified 21 months ago by WouterDeCoster30k • written 21 months ago by hsinyen90
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1436 users visited in the last hour