Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank

The UK Biobank performed whole-genome sequencing (WGS) and whole-exome sequencing (WES) across hundreds of thousands of individuals, allowing researchers to study the effects of both common and rare variants. Haplotype phasing distinguishes the two inherited copies of each chromosome into haplotypes and unlocks novel analyses at the haplotype level. In this work, we describe a new phasing method, SHAPEIT5, that accurately and rapidly phases large sequencing datasets and illustrates its key features on the UK Biobank WGS and WES data. First, we show that it phases rare variants with high accuracy. For instance, variants found in 1 sample out of 100,000 in the WES data are phased with accuracy above 95%. Second, we show that it can phase singletons, although with moderate accuracy, thereby making their inclusion in downstream analyses possible. Third, we show that the use of UK Biobank as a reference panel increases the accuracy of genotype imputation, an increase that is more pronounced when phased with SHAPEIT5 compared to other methods. Finally, we screen the phased WES data for loss-of-function (LoF) compound heterozygous (CH) events and identify 549 genes in which both gene copies are found knocked out. This list of genes complements current knowledge of gene essentiality in the human genome. We provide SHAPEIT5 in an open-source format, providing researchers with the means to leverage haplotype information in genetic studies.