{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T06:10:42Z","timestamp":1783059042515,"version":"3.54.6"},"reference-count":21,"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: The sequencing of tumors and their matched normals is frequently used to study the genetic composition of cancer. Despite this fact, there remains a dearth of available software tools designed to compare sequences in pairs of samples and identify sites that are likely to be unique to one sample.<\/jats:p>\n               <jats:p>Results: In this article, we describe the mathematical basis of our SomaticSniper software for comparing tumor and normal pairs. We estimate its sensitivity and precision, and present several common sources of error resulting in miscalls.<\/jats:p>\n               <jats:p>Availability and implementation: Binaries are freely available for download at http:\/\/gmt.genome.wustl.edu\/somatic-sniper\/current\/, implemented in C and supported on Linux and Mac OS X.<\/jats:p>\n               <jats:p>Contact: \u00a0delarson@wustl.edu; lding@wustl.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr665","type":"journal-article","created":{"date-parts":[[2011,12,8]],"date-time":"2011-12-08T01:24:20Z","timestamp":1323307460000},"page":"311-317","source":"Crossref","is-referenced-by-count":589,"title":["SomaticSniper: identification of somatic point mutations in whole genome sequencing data"],"prefix":"10.1093","volume":"28","author":[{"given":"David E.","family":"Larson","sequence":"first","affiliation":[{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"},{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher C.","family":"Harris","sequence":"additional","affiliation":[{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ken","family":"Chen","sequence":"additional","affiliation":[{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"},{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel C.","family":"Koboldt","sequence":"additional","affiliation":[{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Travis E.","family":"Abbott","sequence":"additional","affiliation":[{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David J.","family":"Dooling","sequence":"additional","affiliation":[{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"},{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy J.","family":"Ley","sequence":"additional","affiliation":[{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"},{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"},{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"},{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elaine R.","family":"Mardis","sequence":"additional","affiliation":[{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"},{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"},{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard K.","family":"Wilson","sequence":"additional","affiliation":[{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"},{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"},{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Ding","sequence":"additional","affiliation":[{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"},{"name":"1 The Genome Institute, 2Department of Genetics, 3Department of Internal Medicine, Division of Oncology and 4Siteman Cancer Center, Washington University, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,12,6]]},"reference":[{"key":"2023012512144210300_B1","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1093\/bioinformatics\/btp624","article-title":"Quantifying uncertainty in genotype calls","volume":"26","author":"Carvalho","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512144210300_B2","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1038\/nature08989","article-title":"Genome remodelling in a basal-like breast cancer metastasis and xenograft","volume":"464","author":"Ding","year":"2010","journal-title":"Nature"},{"key":"2023012512144210300_B3","doi-asserted-by":"crossref","first-page":"D945","DOI":"10.1093\/nar\/gkq929","article-title":"COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer","volume":"39","author":"Forbes","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012512144210300_B4","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1093\/bioinformatics\/btq040","article-title":"SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors","volume":"26","author":"Goya","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512144210300_B5","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1038\/nature05610","article-title":"Patterns of somatic mutation in human cancer genomes","volume":"446","author":"Greenman","year":"2007","journal-title":"Nature"},{"key":"2023012512144210300_B6","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1126\/science.1196333","article-title":"Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma","volume":"330","author":"Jones","year":"2010","journal-title":"Science"},{"key":"2023012512144210300_B7","doi-asserted-by":"crossref","first-page":"2283","DOI":"10.1093\/bioinformatics\/btp373","article-title":"VarScan: variant detection in massively parallel sequencing of individual and pooled samples","volume":"25","author":"Koboldt","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512144210300_B8","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1038\/nature07485","article-title":"DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome","volume":"456","author":"Ley","year":"2008","journal-title":"Nature"},{"key":"2023012512144210300_B9","doi-asserted-by":"crossref","first-page":"2424","DOI":"10.1056\/NEJMoa1005143","article-title":"DNMT3A mutations in acute myeloid leukemia","volume":"363","author":"Ley","year":"2010","journal-title":"N. Engl. J. Med."},{"key":"2023012512144210300_B10","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1101\/gr.078212.108","article-title":"Mapping short DNA sequencing reads and calling variants using mapping quality scores","volume":"18","author":"Li","year":"2008","journal-title":"Genome Res."},{"key":"2023012512144210300_B11","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512144210300_B12","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1101\/gr.088013.108","article-title":"SNP detection for massively parallel whole-genome resequencing","volume":"19","author":"Li","year":"2009","journal-title":"Genome Res."},{"key":"2023012512144210300_B13","doi-asserted-by":"crossref","first-page":"1058","DOI":"10.1056\/NEJMoa0903840","article-title":"Recurring mutations found by sequencing an acute myeloid leukemia genome","volume":"361","author":"Mardis","year":"2009","journal-title":"N. Engl. J. Med."},{"key":"2023012512144210300_B14","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1038\/nature08658","article-title":"A comprehensive catalogue of somatic mutations from a human cancer genome","volume":"463","author":"Pleasance","year":"2010","journal-title":"Nature"},{"key":"2023012512144210300_B15","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1038\/nature08629","article-title":"A small-cell lung cancer genome with complex signatures of tobacco exposure","volume":"463","author":"Pleasance","year":"2010","journal-title":"Nature"},{"key":"2023012512144210300_B16","doi-asserted-by":"crossref","first-page":"2719","DOI":"10.1056\/NEJMoa0902542","article-title":"Mutation of FOXL2 in granulosa-cell tumors of the ovary","volume":"360","author":"Shah","year":"2009","journal-title":"N. Engl. J. Med."},{"key":"2023012512144210300_B17","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1038\/nature08489","article-title":"Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution","volume":"461","author":"Shah","year":"2009","journal-title":"Nature"},{"key":"2023012512144210300_B18","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"Sherry","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023012512144210300_B19","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1186\/1471-2105-9-239","article-title":"Aspects of coverage in medical DNA sequencing","volume":"9","author":"Wendl","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012512144210300_B20","doi-asserted-by":"crossref","first-page":"1532","DOI":"10.1056\/NEJMoa1008433","article-title":"ARID1A mutations in endometriosis-associated ovarian carcinomas","volume":"363","author":"Wiegand","year":"2010","journal-title":"N. Engl. J. Med."},{"key":"2023012512144210300_B21","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1023\/A:1022463111224","article-title":"Beta approximation to the distribution of Kolmogorov-Smirnov statistic","volume":"54","author":"Zhang","year":"2002","journal-title":"Ann. Ins. Stat. Math."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/3\/311\/48874526\/bioinformatics_28_3_311.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/3\/311\/48874526\/bioinformatics_28_3_311.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T14:30:23Z","timestamp":1674657023000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/3\/311\/188933"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,12,6]]},"references-count":21,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2012,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr665","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":[[2011,12,6]]}}}