Hello, I have phased plink files of a population. I would like to obtain all SNPs that are in high linkage disequilibrium (LD) for a set of 10 SNPs. I know how to do it according to a r2 threshold, but I need to set this threshold according to D'
For instance, this script will output all variants in high LD (r2 > 0.6) for a list of 10 SNPs within a range of 1000 Kb.
plink \ --bfile myfile \ --r2 --ld-snp-list list_10_snps.txt \ --ld-window-kb 1000 --ld-window-r2 0.6
Thanks very much