{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:32Z","timestamp":1772138072343,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,3,4]],"date-time":"2025-03-04T00:00:00Z","timestamp":1741046400000},"content-version":"vor","delay-in-days":366,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Chan Zuckerberg Insititute\u2019s Essential Open Source Software Initiative","award":["EOSS4-0000000180"],"award-info":[{"award-number":["EOSS4-0000000180"]}]},{"name":"Chan Zuckerberg Insititute\u2019s Essential Open Source Software Initiative","award":["R01HG012252"],"award-info":[{"award-number":["R01HG012252"]}]},{"name":"National Human Genome Research Insititute"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Variant call format (VCF) files are the standard output format for various software tools that identify genetic variation from DNA sequencing experiments. Downstream analyses require the ability to query, filter, and modify them simply and efficiently. Several tools are available to perform these operations from the command line, including BCFTools, vembrane, slivar, and others.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we introduce vcfexpress, a new, high-performance toolset for the analysis of VCF files, written in the Rust programming language. It is nearly as fast as BCFTools, but adds functionality to execute user expressions in the lua programming language for precise filtering and reporting of variants from a VCF or BCF file. We demonstrate performance and flexibility by comparing vcfexpress to other tools using the vembrane benchmark.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>vcfexpress is available under the MIT license at https:\/\/github.com\/brentp\/vcfexpress with code used for the manuscript deposited in https:\/\/doi.org\/10.5281\/zenodo.14756838.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf097","type":"journal-article","created":{"date-parts":[[2025,2,27]],"date-time":"2025-02-27T08:14:51Z","timestamp":1740644091000},"source":"Crossref","is-referenced-by-count":3,"title":["Vcfexpress: flexible, rapid user-expressions to filter and format VCFs"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1786-2216","authenticated-orcid":false,"given":"Brent S","family":"Pedersen","sequence":"first","affiliation":[{"name":"Department of Human Genetics, University of Utah , Salt Lake City, UT 84112,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1756-0859","authenticated-orcid":false,"given":"Aaron R","family":"Quinlan","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, University of Utah , Salt Lake City, UT 84112,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2024,3,3]]},"reference":[{"key":"2025031307373744100_btaf097-B1","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab007","article-title":"HTSlib: C library for reading\/writing high-throughput sequencing data","volume":"10","author":"Bonfield","year":"2021","journal-title":"Gigascience"},{"key":"2025031307373744100_btaf097-B2","doi-asserted-by":"crossref","first-page":"35","DOI":"10.3389\/fgene.2012.00035","article-title":"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift","volume":"3","author":"Cingolani","year":"2012","journal-title":"Front Genet"},{"key":"2025031307373744100_btaf097-B3","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"2025031307373744100_btaf097-B4","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":"2025031307373744100_btaf097-B5","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"2025031307373744100_btaf097-B6","doi-asserted-by":"crossref","first-page":"e1009123","DOI":"10.1371\/journal.pcbi.1009123","article-title":"A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar","volume":"18","author":"Garrison","year":"2022","journal-title":"PLoS Comput Biol"},{"key":"2025031307373744100_btaf097-B7","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btac810","article-title":"Insane in the vembrane: filtering and transforming VCF\/BCF files","volume":"39","author":"Hartmann","year":"2023","journal-title":"Bioinformatics"},{"key":"2025031307373744100_btaf097-B8","doi-asserted-by":"crossref","first-page":"122","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":"2025031307373744100_btaf097-B9","doi-asserted-by":"crossref","first-page":"60","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 Med"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf097\/62261846\/btaf097.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/3\/btaf097\/62261846\/btaf097.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/3\/btaf097\/62261846\/btaf097.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,13]],"date-time":"2025-03-13T03:37:48Z","timestamp":1741837068000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf097\/8051444"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,3,3]]},"references-count":9,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,3,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf097","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.11.05.622129","asserted-by":"object"}]},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,3]]},"published":{"date-parts":[[2024,3,3]]},"article-number":"btaf097"}}