{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T14:08:33Z","timestamp":1761919713969},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1174,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We have developed Cake, a bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. Cake can be run on a high-performance computer cluster or used as a stand-alone application.<\/jats:p>\n               <jats:p>Availabilty: Cake is open-source and is available from http:\/\/cakesomatic.sourceforge.net\/<\/jats:p>\n               <jats:p>Contact: \u00a0da1@sanger.ac.uk<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt371","type":"journal-article","created":{"date-parts":[[2013,6,27]],"date-time":"2013-06-27T00:32:39Z","timestamp":1372293159000},"page":"2208-2210","source":"Crossref","is-referenced-by-count":27,"title":["Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes"],"prefix":"10.1093","volume":"29","author":[{"given":"Mamunur","family":"Rashid","sequence":"first","affiliation":[{"name":"Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1HH, UK"}]},{"given":"Carla Daniela","family":"Robles-Espinoza","sequence":"additional","affiliation":[{"name":"Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1HH, UK"}]},{"given":"Alistair G.","family":"Rust","sequence":"additional","affiliation":[{"name":"Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1HH, UK"}]},{"given":"David J.","family":"Adams","sequence":"additional","affiliation":[{"name":"Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1HH, UK"}]}],"member":"286","published-online":{"date-parts":[[2013,7,16]]},"reference":[{"key":"2023012810455767400_btt371-B1","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1093\/bioinformatics\/btr032","article-title":"Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM\/BAM format","volume":"27","author":"Edmonson","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810455767400_btt371-B2","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1038\/ng.2256","article-title":"Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma","volume":"44","author":"Guichard","year":"2012","journal-title":"Nat. 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