{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T02:04:51Z","timestamp":1771293891310,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Storing, annotating and analyzing variants from next-generation sequencing projects can be difficult due to the availability of a wide array of data formats, tools and annotation sources, as well as the sheer size of the data files. Useful tools, including the GATK, ANNOVAR and BEDTools can be integrated into custom pipelines for annotating and analyzing sequence variants. However, building flexible pipelines that support the tracking of variants alongside their samples, while enabling updated annotation and reanalyses, is not a simple task.<\/jats:p>\n               <jats:p>Results: We have developed variant tools, a flexible annotation and analysis toolset that greatly simplifies the storage, annotation and filtering of variants and the analysis of the underlying samples. variant tools can be used to manage and analyze genetic variants obtained from sequence alignments, and the command-line driven toolset could be used as a foundation for building more sophisticated analytical methods.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0variant tools consists of two command-line driven programs vtools and vtools_report. It is freely available at http:\/\/varianttools.sourceforge.net, distributed under a GPL license.<\/jats:p>\n               <jats:p>Contact: \u00a0bpeng@mdanderson.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr667","type":"journal-article","created":{"date-parts":[[2011,12,4]],"date-time":"2011-12-04T01:24:53Z","timestamp":1322961893000},"page":"421-422","source":"Crossref","is-referenced-by-count":124,"title":["Integrated annotation and analysis of genetic variants from next-generation sequencing studies with <i>variant tools<\/i>"],"prefix":"10.1093","volume":"28","author":[{"given":"F. Anthony","family":"San Lucas","sequence":"first","affiliation":[{"name":"1 Department of Epidemiology, University of Texas, MD Anderson Cancer Center, 2Program in Biomathematics and Biostatistics, University of Texas Graduate School of Biomedical Sciences and 3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA, 4Department of Genetics, University of Texas, MD Anderson Cancer Center"},{"name":"1 Department of Epidemiology, University of Texas, MD Anderson Cancer Center, 2Program in Biomathematics and Biostatistics, University of Texas Graduate School of Biomedical Sciences and 3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA, 4Department of Genetics, University of Texas, MD Anderson Cancer Center"}]},{"given":"Gao","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology, University of Texas, MD Anderson Cancer Center, 2Program in Biomathematics and Biostatistics, University of Texas Graduate School of Biomedical Sciences and 3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA, 4Department of Genetics, University of Texas, MD Anderson Cancer Center"}]},{"given":"Paul","family":"Scheet","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology, University of Texas, MD Anderson Cancer Center, 2Program in Biomathematics and Biostatistics, University of Texas Graduate School of Biomedical Sciences and 3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA, 4Department of Genetics, University of Texas, MD Anderson Cancer Center"},{"name":"1 Department of Epidemiology, University of Texas, MD Anderson Cancer Center, 2Program in Biomathematics and Biostatistics, University of Texas Graduate School of Biomedical Sciences and 3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA, 4Department of Genetics, University of Texas, MD Anderson Cancer Center"}]},{"given":"Bo","family":"Peng","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology, University of Texas, MD Anderson Cancer Center, 2Program in Biomathematics and Biostatistics, University of Texas Graduate School of Biomedical Sciences and 3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA, 4Department of Genetics, University of Texas, MD Anderson Cancer Center"}]}],"member":"286","published-online":{"date-parts":[[2011,12,2]]},"reference":[{"key":"2023012512170135700_B1","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"},{"issue":"Suppl. 1","key":"2023012512170135700_B2","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gkj144","article-title":"The UCSC genome browser database: update 2006","volume":"34","author":"Hinrichs","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012512170135700_B3","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023012512170135700_B4","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1002\/humu.21517","article-title":"dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions","volume":"32","author":"Liu","year":"2011","journal-title":"Hum. Mutat."},{"key":"2023012512170135700_B5","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512170135700_B6","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/3\/421\/48879065\/bioinformatics_28_3_421.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/3\/421\/48879065\/bioinformatics_28_3_421.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T14:47:54Z","timestamp":1674658074000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/3\/421\/189037"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,12,2]]},"references-count":6,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2012,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr667","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,2,1]]},"published":{"date-parts":[[2011,12,2]]}}}