I have two lists of SNPs, List A and List B, I want to calculate r2 of each SNP in A with each SNP in B in a pairwise manner.
None of the tools I know allow that, I can play with awk to create a single file with all pairwise pairs but then I am wondering which tool could be the best to give the generated file as Input, plink ? the problem with plink is that I never understood what is the my data file is, like in this command
plink --bfile mydata --ld rs2840528 rs7545940
Any idea is welcome
We use Haploview. It is free and one of if not the best for this. It should be easy for Haploview to take you list of SNPs as a single file, after which you can look for the LD between distinct pairs.
To calculate LD with accuracy, you need genotypes from at least 50 unrelated individuals.
You can use SNAP from Broad to get pairwise LD between two SNPs or a list of SNPs.
You can also find other SNPs that are in LD (proxySNPs) for your SNPs. You can use specific populations, (different hapmap datasets including 1000genomes).
You can also find if those SNPs have membership in major commercial array platforms. I use it all the time and like it very much.