{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:17Z","timestamp":1740185117080,"version":"3.37.3"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2018,1,15]],"date-time":"2018-01-15T00:00:00Z","timestamp":1515974400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005972","name":"Deutsche Krebshilfe","doi-asserted-by":"publisher","award":["110495"],"award-info":[{"award-number":["110495"]}],"id":[{"id":"10.13039\/501100005972","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>With the rapid development in next-generation sequencing, cost and time requirements for genomic sequencing are decreasing, enabling applications in many areas such as cancer research. Many tools have been developed to analyze genomic variation ranging from single nucleotide variants to whole chromosomal aberrations. As sequencing throughput increases, the number of variants called by such tools also grows. Often employed manual inspection of such calls is thus becoming a time-consuming procedure. We developed the Variant InsPector and Expert Rating tool (VIPER) to speed up this process by integrating the Integrative Genomics Viewer into a web application. Analysts can then quickly iterate through variants, apply filters and make decisions based on the generated images and variant metadata. VIPER was successfully employed in analyses with manual inspection of more than 10 000 calls.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>VIPER is implemented in Java and Javascript and is freely available at https:\/\/github.com\/MarWoes\/viper.<\/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\/bty022","type":"journal-article","created":{"date-parts":[[2018,1,12]],"date-time":"2018-01-12T20:27:55Z","timestamp":1515788875000},"page":"1928-1929","source":"Crossref","is-referenced-by-count":7,"title":["VIPER: a web application for rapid expert review of variant calls"],"prefix":"10.1093","volume":"34","author":[{"given":"Marius","family":"W\u00f6ste","sequence":"first","affiliation":[{"name":"Institute of Medical Informatics, University of M\u00fcnster, M\u00fcnster, Germany"}]},{"given":"Martin","family":"Dugas","sequence":"additional","affiliation":[{"name":"Institute of Medical Informatics, University of M\u00fcnster, M\u00fcnster, Germany"}]}],"member":"286","published-online":{"date-parts":[[2018,1,15]]},"reference":[{"key":"2023012713563144400_bty022-B1","doi-asserted-by":"crossref","first-page":"17875.","DOI":"10.1038\/srep17875","article-title":"Systematic comparison of variant calling pipelines using gold standard personal exome variants","volume":"5","author":"Hwang","year":"2016","journal-title":"Sci. Rep"},{"key":"2023012713563144400_bty022-B2","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: a mapreduce framework for analyzing next-generation dna sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res"},{"key":"2023012713563144400_bty022-B3","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol"},{"key":"2023012713563144400_bty022-B4","doi-asserted-by":"crossref","first-page":"43169.","DOI":"10.1038\/srep43169","article-title":"Evaluating variant calling tools for non-matched next-generation sequencing data","volume":"7","author":"Sandmann","year":"2017","journal-title":"Sci. Rep"},{"key":"2023012713563144400_bty022-B5","doi-asserted-by":"crossref","first-page":"215.","DOI":"10.3389\/fgene.2015.00215","article-title":"Clinical applications of next generation sequencing in cancer: from panels, to exomes, to genomes","volume":"6","author":"Shen","year":"2015","journal-title":"Front. Genet"},{"key":"2023012713563144400_bty022-B6","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsd\u00f3ttir","year":"2013","journal-title":"Brief. Bioinf"},{"key":"2023012713563144400_bty022-B7","doi-asserted-by":"crossref","first-page":"2865","DOI":"10.1093\/bioinformatics\/btp394","article-title":"Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads","volume":"25","author":"Ye","year":"2009","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/11\/1928\/48937809\/bioinformatics_34_11_1928.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/11\/1928\/48937809\/bioinformatics_34_11_1928.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T14:28:37Z","timestamp":1674829717000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/11\/1928\/4810439"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,1,15]]},"references-count":7,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2018,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty022","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,6,1]]},"published":{"date-parts":[[2018,1,15]]}}}