Multiallelic Maximal Perfect Haplotype Blocks with Wildcards via PBWT

Computing maximal perfect blocks of a given panel of haplotypes is a crucial task for efficiently solving problems such as polyploid haplotype reconstruction and finding identical-by-descent segments shared among individuals of a population. Unfortunately, the presence of missing data in the haplotype panel limits the usefulness of the notion of perfect blocks. We propose a novel algorithm for computing maximal blocks in a panel with missing data (represented as wildcards). The algorithm is based on the Positional Burrows-Wheeler Transform (PBWT) and has been implemented in the tool Wild-pBWT, available at https://github.com/AlgoLab/Wild-pBWT/. Experimental comparison showed that Wild-pBWT is 10–15 times faster than another state-of-the-art approach, while using a negligible amount of memory.