Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin analyses.

ABSTRACT: Haplotype phasing, the process of determining which genetic variants are physically located on the same chromosome, is crucial for genetic analyses. Here, we benchmark SHAPEIT and Beagle, two state-of-the-art phasing methods, on two large datasets: >8 million research-consented 23andMe, Inc. customers and the UK Biobank (UKB). Remarkably, both methods' median switch error rate (SER) (after excluding single SNP switches, which we call "blips") is 0.00% across all tested 23andMe trio children and 0.026% in British samples from UKB. Across UKB samples, switch errors predominantly occur in regions lacking identity-by-descent (IBD) coverage. SHAPEIT and Beagle excel at intra-chromosomal phasing, but lack the ability to phase across chromosomes, motivating us to develop HAPTiC (HAPlotype Tiling

SUBMITTER: Williams CM 

PROVIDER: S-EPMC12536663 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature