I am estimating the pairwise r^2 LD estimator between SNPs I have selected for a SNP chip. I would like to estimate this r^2 between any pair of SNPs selected despite their location in different scaffolds. (I have several genotypes for each marker). I am using vcftools to do so. Otherwise I get only the r2 estimates between SNPs within the same scaffold. Does anyone know how to do it between any pair of SNPs, regardless of the situation?
Thanks a lot in advance, best!