Optimal Linkage Disequilibrium Splitting

Motivation A few algorithms have been developed for splitting the genome in nearly independent blocks of linkage disequilibrium. Due to the complexity of this problem, these algorithms rely on heuristics, which makes them sub-optimal. Results Here we develop an optimal solution for this problem using dynamic programming. Availability This is now implemented as function snp_ldplit as part of R package bigsnpr. Supplementary information Supplementary data are available at Bioinformatics online.