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Improving population scale statistical phasing with whole-genome sequencing data.
Wertenbroek, Rick; Hofmeister, Robin J; Xenarios, Ioannis; Thoma, Yann; Delaneau, Olivier.
Afiliación
  • Wertenbroek R; University of Lausanne, Lausanne, Vaud, Switzerland.
  • Hofmeister RJ; School of Engineering and Management Vaud (HEIG-VD), HES-SO University of Applied Sciences and Arts Western Switzerland, Yverdon-les-Bains, Vaud, Switzerland.
  • Xenarios I; University of Lausanne, Lausanne, Vaud, Switzerland.
  • Thoma Y; University of Lausanne, Lausanne, Vaud, Switzerland.
  • Delaneau O; School of Engineering and Management Vaud (HEIG-VD), HES-SO University of Applied Sciences and Arts Western Switzerland, Yverdon-les-Bains, Vaud, Switzerland.
PLoS Genet ; 20(7): e1011092, 2024 Jul.
Article en En | MEDLINE | ID: mdl-38959269
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 by refining haplotype estimates through the realignment of sequencing reads, particularly targeting low-confidence phase calls. Our findings demonstrate that SAPPHIRE significantly enhances the accuracy of haplotypes obtained from state of the art methods and also provides the subset of phase calls that are validated by sequencing reads. Finally, we show that our method scales to large data sets by its successful application to the extensive 3.6 Petabytes of sequencing data of the last UK Biobank 200,031 sample release.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Haplotipos / Secuenciación Completa del Genoma / Genética de Población Límite: Humans Idioma: En Revista: PLoS Genet Asunto de la revista: GENETICA Año: 2024 Tipo del documento: Article País de afiliación: Suiza

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Haplotipos / Secuenciación Completa del Genoma / Genética de Población Límite: Humans Idioma: En Revista: PLoS Genet Asunto de la revista: GENETICA Año: 2024 Tipo del documento: Article País de afiliación: Suiza