{"doi":"10.1038/ng.3679","title":"Reference-based phasing using the Haplotype Reference Consortium panel","abstract":"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 ∼20× speedup and ∼10% increase in accuracy compared to reference-based phasing using SHAPEIT2. On European-ancestry samples, Eagle2 with the HRC panel achieves >2× 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.","journal":"Nature Genetics","year":2016,"id":10394,"datarank":13.807256006137873,"base_score":7.59488438721652,"endowment":7.59488438721652,"self_citation_contribution":1.139232658082478,"citation_network_contribution":12.668023348055396,"self_endowment_contribution":1.139232658082478,"citer_contribution":12.668023348055396,"corpus_percentile":83.3,"corpus_rank":2568,"citation_count":1987,"citer_count":178,"citers_with_citation_signal":178,"citers_with_endowment":178,"datacite_reuse_total":0,"is_dataset":false,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2016-10-03","authors":[{"id":61903,"name":"Chris O’Sullivan","orcid":"0000-0002-3179-1250","position":1,"is_corresponding":false},{"id":24618,"name":"Pier Francesco Palamara","orcid":"0000-0002-7999-1972","position":2,"is_corresponding":false},{"id":16065,"name":"Christian Fuchsberger","orcid":"0000-0002-5918-8947","position":3,"is_corresponding":false},{"id":86759,"name":"Yakir A Reshef","orcid":null,"position":4,"is_corresponding":false},{"id":3039,"name":"Hilary K. Finucane","orcid":"0000-0003-3864-9828","position":5,"is_corresponding":false},{"id":86760,"name":"Sebastian Schoenherr","orcid":null,"position":6,"is_corresponding":false},{"id":86761,"name":"Lukas Forer","orcid":"0000-0003-2139-7329","position":7,"is_corresponding":false},{"id":15623,"name":"Shane A McCarthy","orcid":"0000-0002-2715-4187","position":8,"is_corresponding":false},{"id":22009,"name":"Joel N. Hirschhorn","orcid":"0000-0002-1650-7901","position":9,"is_corresponding":false},{"id":2123,"name":"Richard Durbin","orcid":"0000-0002-9130-1006","position":10,"is_corresponding":false},{"id":22002,"name":"Alkes L. Price","orcid":"0000-0002-2971-7975","position":11,"is_corresponding":false},{"id":24619,"name":"Po‐Ru Loh","orcid":"0000-0001-5542-9064","position":12,"is_corresponding":false},{"id":86424,"name":"Yakir Reshef","orcid":"0000-0001-6463-4203","position":13,"is_corresponding":false},{"id":14736,"name":"Gonçalo R. Abecasis","orcid":"0000-0003-1509-1825","position":14,"is_corresponding":false}],"reference_count":31,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}