I am trying to compute haplotype blocks using PLINK. I found this function very useful
--blocks, as it outputs the haplotypes (with the corresponding SNPs within it) in rows and not as a table (as when using
--r2). However, it uses D-prime to estimate LD between SNPs.
Is it possible to get haplotype blocks defined by say SNPs with r2 > 0.8 in the same format i.e. haplotypes by rows with the list of SNPs within each haplotype, and not a pair-wise LD table?