{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:17Z","timestamp":1772138057180,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,15]],"date-time":"2022-12-15T00:00:00Z","timestamp":1671062400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Research Foundation collaborative Research Center 876","award":["124020371"],"award-info":[{"award-number":["124020371"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>We present vembrane as a command line variant call format (VCF)\/binary call format (BCF) filtering tool that consolidates and extends the filtering functionality of previous software to meet any imaginable filtering use case. Vembrane exposes the VCF\/BCF file type specification and its inofficial extensions by the annotation tools VEP and SnpEff as Python data structures. vembrane filter enables filtration by Python expressions, requiring only basic knowledge of the Python programming language. vembrane table allows users to generate tables from subsets of annotations or functions thereof. Finally, it is fast, by using pysam and relying on lazy evaluation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Source code and installation instructions are available at github.com\/vembrane\/vembrane (doi: 10.5281\/zenodo.7003981).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac810","type":"journal-article","created":{"date-parts":[[2022,12,14]],"date-time":"2022-12-14T18:04:27Z","timestamp":1671041067000},"source":"Crossref","is-referenced-by-count":6,"title":["Insane in the vembrane: filtering and transforming VCF\/BCF files"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6993-347X","authenticated-orcid":false,"given":"Till","family":"Hartmann","sequence":"first","affiliation":[{"name":"Algorithms for Reproducible Bioinformatics, University Hospital Essen, University of Duisburg-Essen , Essen 45147, Germany"}]},{"given":"Christopher","family":"Schr\u00f6der","sequence":"additional","affiliation":[{"name":"Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen , Essen 45147, Germany"}]},{"given":"Elias","family":"Kuthe","sequence":"additional","affiliation":[{"name":"Computer Science XI, TU Dortmund University , Dortmund 44227, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9138-4112","authenticated-orcid":false,"given":"David","family":"L\u00e4hnemann","sequence":"additional","affiliation":[{"name":"Algorithms for Reproducible Bioinformatics, University Hospital Essen, University of Duisburg-Essen , Essen 45147, Germany"},{"name":"Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen , Essen 45147, Germany"}]},{"given":"Johannes","family":"K\u00f6ster","sequence":"additional","affiliation":[{"name":"Algorithms for Reproducible Bioinformatics, University Hospital Essen, University of Duisburg-Essen , Essen 45147, Germany"},{"name":"Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215, USA"}]}],"member":"286","published-online":{"date-parts":[[2022,12,15]]},"reference":[{"key":"2023010805403969600_btac810-B1","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"Program for annotating and predicting the effects of single nucleotide polymorphisms","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"2023010805403969600_btac810-B2","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"2023010805403969600_btac810-B3","author":"Garrison","year":"2021"},{"key":"2023010805403969600_btac810-B4","doi-asserted-by":"crossref","first-page":"1224","DOI":"10.1093\/bioinformatics\/btx734","article-title":"Bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files","volume":"34","author":"Lindenbaum","year":"2018","journal-title":"Bioinformatics"},{"key":"2023010805403969600_btac810-B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-016-0974-4","article-title":"The ensembl variant effect predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol"},{"key":"2023010805403969600_btac810-B6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41525-021-00227-3","article-title":"Effective variant filtering and expected candidate variant yield in studies of rare human disease","volume":"6","author":"Pedersen","year":"2021","journal-title":"NPJ Genom. 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Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac810\/48361915\/btac810.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btac810\/48520818\/btac810.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btac810\/48520818\/btac810.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T00:40:58Z","timestamp":1673138458000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btac810\/6909012"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,12,15]]},"references-count":7,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac810","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.08.17.504106","asserted-by":"object"}]},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,1]]},"published":{"date-parts":[[2022,12,15]]},"article-number":"btac810"}}