SLAB: A Sweep Line Algorithm in PBWT for Finding Haplotype Block Cores

With the increasing availability of high-quality phased haplotype data, researchers can more effectively identify detailed patterns of haplotype sharing and investigate the population genetic processes that shape them. In this work, we define block cores as genomic segments where multiple haplotype blocks overlap. We develop an efficient algorithm to analyze haplotype blocks, focusing on width-maximal matches and the identification of haplotype block cores. We apply our algorithm to UK Biobank haplotypes to quantify block cores and demonstrate the biological and population-level insights that can be inferred from their patterns. Specifically, identified block cores can serve as a basis for detecting signals of selection. Although our results are largely consistent with those from methods such as IBD rate analysis, they also reveal complementary information not captured by IBD rates or other conventional approaches. Source code is available at https://github.com/ZhiGroup/SLAB.