期刊
NATURE GENETICS
卷 48, 期 11, 页码 1443-1448出版社
NATURE PORTFOLIO
DOI: 10.1038/ng.3679
关键词
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资金
- US National Institutes of Health [R01 HG006399, R01 MH101244, HG007022, HL117626]
- Wellcome Trust [WT098051]
- Austrian Science Fund (FWF) [J-3401]
- Fannie and John Hertz Foundation
- NCRR [1S10RR028832-01]
- Netherlands Scientific Organization [NWO 480-05-003]
- [F32 HG007805]
- MRC [G0801823] Funding Source: UKRI
- Medical Research Council [G0801823, MC_qA137853] Funding Source: researchfish
Haplotype phasing is a fundamental problem in medical and population genetics. Phasing is generally performed via statistical phasing in a genotyped cohort, an approach that can yield high accuracy in very large cohorts but attains lower accuracy in smaller cohorts. Here we instead explore the paradigm of reference-based phasing. We introduce a new phasing algorithm, Eagle2, that attains high accuracy across a broad range of cohort sizes by efficiently leveraging information from large external reference panels (such as the Haplotype Reference Consortium; HRC) using a new data structure based on the positional Burrows-Wheeler transform. We demonstrate that Eagle2 attains a similar to 20x speedup and similar to 10% increase in accuracy compared to reference-based phasing using SHAPEIT2. On European ancestry samples, Eagle2 with the HRC panel achieves >2x the accuracy of 1000 Genomes-based phasing. Eagle2 is open source and freely available for HRC-based phasing via the Sanger Imputation Service and the Michigan Imputation Server.
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