Is there a tool which can generate haplotype blocks (with plot, like Haploview) without genotype data? I only have a list of SNPs. Thanks!
Given that LD is the non-random association of alleles at different loci, I would say: NO!
However, if you are working in human and you have a list of SNPs, maybe you can browse the 1000 genome data and see if they share haplotype blocks data (I think they do, but I do not know where).
You could use LDLink's LDMatrix and select the appropriate population
Thanks! It works perfectly. However, is it possible to draw a triangular matrix (since it's symmetric) rather than a square matrix?