LD score is defined as the sum of LD r2 between a variant and all the variants in a region.
I want to estimate the LD score for an arbitrary numbers of SNPs in a PLINK format dataset that I have. I was simply planning to get the LD between all snps to get the LDscore. I am trying to do this using this command, but I get an empty output:
plink --bfile myfile --extract snps_to_calculate_ldscore.txt \ --r2 --ld-window-kb 9999999 \ --ld-window-r2 0 --out ldscore