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