{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T12:56:57Z","timestamp":1770814617640,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2020,8,5]],"date-time":"2020-08-05T00:00:00Z","timestamp":1596585600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"NIH\/NHGRI","award":["R01HG008983"],"award-info":[{"award-number":["R01HG008983"]}]},{"name":"NIH\/NHGRI","award":["R01GM126479"],"award-info":[{"award-number":["R01GM126479"]}]},{"name":"NIH\/NIGMS"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,8]]},"abstract":"Abstract<\/jats:title>\n \n Summary<\/jats:title>\n Here, we present a highly efficient R-package seqminer2 for querying and retrieving sequence variants from biobank scale datasets of millions of individuals and hundreds of millions of genetic variants. Seqminer2 implements a novel variant-based index for querying VCF\/BCF files. It improves the speed of query and retrieval by several magnitudes compared to the state-of-the-art tools based upon tabix. It also reimplements support for BGEN and PLINK format, which improves speed over alternative implementations. The improved efficiency and comprehensive support for popular file formats will facilitate method development, software prototyping and data analysis of biobank scale sequence datasets in R.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n The seqminer2 R package is available from https:\/\/github.com\/zhanxw\/seqminer. Scripts used for the benchmarks are available in https:\/\/github.com\/yang-lina\/seqminer\/blob\/master\/seqminer2%20benchmark%20script.txt.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa628","type":"journal-article","created":{"date-parts":[[2020,7,3]],"date-time":"2020-07-03T19:35:32Z","timestamp":1593804932000},"page":"4951-4954","source":"Crossref","is-referenced-by-count":4,"title":["Seqminer2: an efficient tool to query and retrieve genotypes for statistical genetics analyses from biobank scale sequence dataset"],"prefix":"10.1093","volume":"36","author":[{"given":"Lina","family":"Yang","sequence":"first","affiliation":[{"name":"Department of Public Health Sciences, Penn State College of Medicine , Hershey, PA 17033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuang","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Clinical Science, University of Texas Southwestern Medical Center , Dallas, TX 75390, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bibo","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Public Health Sciences, Penn State College of Medicine , Hershey, PA 17033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dajiang J","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Public Health Sciences, Penn State College of Medicine , Hershey, PA 17033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaowei","family":"Zhan","sequence":"additional","affiliation":[{"name":"Department of Clinical Science, University of Texas Southwestern Medical Center , Dallas, TX 75390, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,8,5]]},"reference":[{"key":"2023062408065561900_btaa628-B1","author":"Band","year":"2018"},{"key":"2023062408065561900_btaa628-B2","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/s41586-018-0579-z","article-title":"The UK Biobank resource with deep phenotyping and genomic data","volume":"562","author":"Bycroft","year":"2018","journal-title":"Nature"},{"key":"2023062408065561900_btaa628-B3","author":"Clayton","year":"2019"},{"key":"2023062408065561900_btaa628-B4","author":"Grueneberg","year":"2019"},{"key":"2023062408065561900_btaa628-B5","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1038\/nmeth.3654","article-title":"Efficient genotype compression and analysis of large genetic-variation data sets","volume":"13","author":"Layer","year":"2016","journal-title":"Nat. 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