{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T19:06:58Z","timestamp":1783969618787,"version":"3.55.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,1,23]],"date-time":"2024-01-23T00:00:00Z","timestamp":1705968000000},"content-version":"vor","delay-in-days":22,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG006855"],"award-info":[{"award-number":["R01HG006855"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01MH104964"],"award-info":[{"award-number":["R01MH104964"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01MH123451"],"award-info":[{"award-number":["R01MH123451"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Many genetics studies report results tied to genomic coordinates of a legacy genome assembly. However, as assemblies are updated and improved, researchers are faced with either realigning raw sequence data using the updated coordinate system or converting legacy datasets to the updated coordinate system to be able to combine results with newer datasets. Currently available tools to perform the conversion of genetic variants have numerous shortcomings, including poor support for indels and multi-allelic variants, that lead to a higher rate of variants being dropped or incorrectly converted. As a result, many researchers continue to work with and publish using legacy genomic coordinates.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here we present BCFtools\/liftover, a tool to convert genomic coordinates across genome assemblies for variants encoded in the variant call format with improved support for indels represented by different reference alleles across genome assemblies and full support for multi-allelic variants. It further supports variant annotation fields updates whenever the reference allele changes across genome assemblies. The tool has the lowest rate of variants being dropped with an order of magnitude less indels dropped or incorrectly converted and is an order of magnitude faster than other tools typically used for the same task. It is particularly suited for converting variant callsets from large cohorts to novel telomere-to-telomere assemblies as well as summary statistics from genome-wide association studies tied to legacy genome assemblies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The tool is written in C and freely available under the MIT open source license as a BCFtools plugin available at http:\/\/github.com\/freeseek\/score.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae038","type":"journal-article","created":{"date-parts":[[2024,1,23]],"date-time":"2024-01-23T18:43:50Z","timestamp":1706035430000},"source":"Crossref","is-referenced-by-count":105,"title":["BCFtools\/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3066-5575","authenticated-orcid":false,"given":"Giulio","family":"Genovese","sequence":"first","affiliation":[{"name":"Program in Medical and Population Genetics, Broad Institute of MIT and Harvard , Cambridge, MA 02142, United States"},{"name":"Stanley Center, Broad Institute of MIT and Harvard , Cambridge, MA 02142, United States"},{"name":"Department of Genetics, Harvard Medical School , Boston, MA 02115, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5249-5357","authenticated-orcid":false,"given":"Nicole B","family":"Rockweiler","sequence":"additional","affiliation":[{"name":"Program in Medical and Population Genetics, Broad Institute of MIT and Harvard , Cambridge, MA 02142, United States"},{"name":"Stanley Center, Broad Institute of MIT and Harvard , Cambridge, MA 02142, United States"},{"name":"Department of Genetics, Harvard Medical School , Boston, MA 02115, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4239-4672","authenticated-orcid":false,"given":"Bryan R","family":"Gorman","sequence":"additional","affiliation":[{"name":"Center for Data and Computational Sciences, VA Boston HealthCare System , Boston, MA 02130, United States"},{"name":"Booz Allen Hamilton Inc , McLean, VA 22102, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2215-5946","authenticated-orcid":false,"given":"Tim B","family":"Bigdeli","sequence":"additional","affiliation":[{"name":"Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University , Brooklyn, NY 11203, United States"},{"name":"Institute for Genomics in Health, SUNY Downstate Health Sciences University , Brooklyn, NY 11203, United States"},{"name":"Cooperative Studies Program, VA New York Harbor Healthcare System , Brooklyn, NY 11209, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle T","family":"Pato","sequence":"additional","affiliation":[{"name":"Department of Psychiatry, Robert Wood Johnson Medical School , New Brunswick, NJ 08901, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5858-266X","authenticated-orcid":false,"given":"Carlos N","family":"Pato","sequence":"additional","affiliation":[{"name":"Department of Psychiatry, Robert Wood Johnson Medical School , New Brunswick, NJ 08901, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-5860-0488","authenticated-orcid":false,"given":"Kiku","family":"Ichihara","sequence":"additional","affiliation":[{"name":"Stanley Center, Broad Institute of MIT and Harvard , Cambridge, MA 02142, United States"},{"name":"Department of Genetics, Harvard Medical School , Boston, MA 02115, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6954-8184","authenticated-orcid":false,"given":"Steven A","family":"McCarroll","sequence":"additional","affiliation":[{"name":"Program in Medical and Population Genetics, Broad Institute of MIT and Harvard , Cambridge, MA 02142, United States"},{"name":"Stanley Center, Broad Institute of MIT and Harvard , Cambridge, MA 02142, United States"},{"name":"Department of Genetics, Harvard Medical School , Boston, MA 02115, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,1,23]]},"reference":[{"key":"2024020112522847400_btae038-B1","doi-asserted-by":"crossref","DOI":"10.1126\/science.abl3533","article-title":"A complete reference genome improves analysis of human genetic 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