{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T06:59:17Z","timestamp":1767855557098,"version":"3.49.0"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2017,7,7]],"date-time":"2017-07-07T00:00:00Z","timestamp":1499385600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,11,1]]},"abstract":"Abstract<\/jats:title>\n \n Summary<\/jats:title>\n The decreasing cost in high-throughput technologies led to a number of sequencing projects consisting of thousands of whole genomes. The paradigm shift from exome to whole genome brings a significant increase in the size of output files. Most of the existing tools which are developed to analyse exome files are not adequate for larger VCF files produced by whole genome studies. In this work we present VCF-Explorer, a variant analysis software capable of handling large files. Memory efficiency and avoiding computationally costly pre-processing step enable to carry out the analysis to be performed with ordinary computers. VCF-Explorer provides an easy to use environment where users can define various types of queries based on variant and sample genotype level annotations. VCF-Explorer can be run in different environments and computational platforms ranging from a standard laptop to a high performance server.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n VCF-Explorer is freely available at: http:\/\/vcfexplorer.sourceforge.net\/.<\/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\/btx422","type":"journal-article","created":{"date-parts":[[2017,7,6]],"date-time":"2017-07-06T11:11:39Z","timestamp":1499339499000},"page":"3468-3470","source":"Crossref","is-referenced-by-count":15,"title":["VCF-Explorer: filtering and analysing whole genome VCF files"],"prefix":"10.1093","volume":"33","author":[{"given":"Mete","family":"Akg\u00fcn","sequence":"first","affiliation":[{"name":"The Scientific and Technological Research Council of Turkey (T\u00dcB\u0130TAK), Gebze, Kocaeli, Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"H\u00fcseyin","family":"Demirci","sequence":"additional","affiliation":[{"name":"The Scientific and Technological Research Council of Turkey (T\u00dcB\u0130TAK), Gebze, Kocaeli, Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,7,7]]},"reference":[{"key":"2023051506353383800_btx422-B1","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bau098","article-title":"Canvasdb: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects","volume":"2014","author":"Ameur","year":"2014","journal-title":"Database"},{"key":"2023051506353383800_btx422-B2","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"Consortium","year":"2015","journal-title":"Nature"},{"key":"2023051506353383800_btx422-B3","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1093\/bib\/bbv051","article-title":"VCF-miner: GUI-based application for mining variants and annotations stored in VCF files","volume":"17","author":"Hart","year":"2016","journal-title":"Brief. Bioinform"},{"key":"2023051506353383800_btx422-B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pcbi.1003153","article-title":"Gemini: integrative exploration of genetic variation and genome annotations","volume":"9","author":"Paila","year":"2013","journal-title":"PLoS Comput. Biol"},{"key":"2023051506353383800_btx422-B5","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbw054","article-title":"BrowseVCF: a web-based application and workflow to quickly prioritize disease-causative variants in VCF files","author":"Salatino","year":"2016","journal-title":"Brief. Bioinform."},{"key":"2023051506353383800_btx422-B6","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1093\/bioinformatics\/btr711","article-title":"VarSifter: visualizing and analyzing exome-scale sequence variation data on a desktop computer","volume":"28","author":"Teer","year":"2012","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/21\/3468\/50315407\/bioinformatics_33_21_3468.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/21\/3468\/50315407\/bioinformatics_33_21_3468.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T06:35:44Z","timestamp":1684132544000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/21\/3468\/3931856"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2017,7,7]]},"references-count":6,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2017,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx422","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,11,1]]},"published":{"date-parts":[[2017,7,7]]}}}