Improving population scale statistical phasing with whole-genome sequencing data.

ABSTRACT: Haplotype estimation, or phasing, has gained significant traction in large-scale projects due to its valuable contributions to population genetics, variant analysis, and the creation of reference panels for imputation and phasing of new samples. To scale with the growing number of samples, haplotype estimation methods designed for population scale rely on highly optimized statistical models to phase genotype data, and usually ignore read-level information. Statistical methods excel in resolving common variants, however, they still struggle at rare variants due to the lack of statistical information. In this study we introduce SAPPHIRE, a new method that leverages whole-genome sequencing data to enhance the precision of haplotype calls produced by statistical phasing. SAPPHIRE achieves this

SUBMITTER: Wertenbroek R 

PROVIDER: S-EPMC11251608 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature