Question: Computing pair-wise R-squared using PLINK (or other packages)

0

hsinyen9 •

**0**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: http://pngu.mgh.harvard.edu/~purcell/plink/ld.shtml

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!

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modified 2.4 years ago
by
WouterDeCoster ♦

**36k**• written 2.4 years ago by hsinyen9 •**0**