Haplotype estimation for biobank scale datasets

The UK Biobank (UKB) has recently released genotypes on 152,328 individuals together with extensive phenotypic and lifestyle information. We present a new phasing method SHAPEIT3 that can handle such biobank scale datasets and results in switch error rates as low as ~0.3%. The method exhibits O(NlogN) scaling in sample size (N), enabling fast and accurate phasing of even larger cohorts.