PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

MotivationLinkage disequilibrium (LD) decay is of great interest in population genetic studies. However, no tool is available now to do LD decay analysis from variant call format (VCF) files directly. In addition, generation of pair-wise LD measurements for whole genome SNPs usually resulting in large storage wasting files.