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!