{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T19:05:22Z","timestamp":1782932722298,"version":"3.54.5"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Massively parallel sequencing technologies hold incredible promise for the study of DNA sequence variation, particularly the identification of variants affecting human disease. The unprecedented throughput and relatively short read lengths of Roche\/454, Illumina\/Solexa, and other platforms have spurred development of a new generation of sequence alignment algorithms. Yet detection of sequence variants based on short read alignments remains challenging, and most currently available tools are limited to a single platform or aligner type. We present VarScan, an open source tool for variant detection that is compatible with several short read aligners. We demonstrate VarScan's ability to detect SNPs and indels with high sensitivity and specificity, in both Roche\/454 sequencing of individuals and deep Illumina\/Solexa sequencing of pooled samples.<\/jats:p>\n               <jats:p>Availability and Implementation: Source code and documentation freely available at http:\/\/genome.wustl.edu\/tools\/cancer-genomics implemented as a Perl package and supported on Linux\/UNIX, MS Windows and Mac OSX.<\/jats:p>\n               <jats:p>Contact: \u00a0dkoboldt@genome.wustl.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp373","type":"journal-article","created":{"date-parts":[[2009,6,20]],"date-time":"2009-06-20T00:30:54Z","timestamp":1245457854000},"page":"2283-2285","source":"Crossref","is-referenced-by-count":1220,"title":["VarScan: variant detection in massively parallel sequencing of individual and pooled samples"],"prefix":"10.1093","volume":"25","author":[{"given":"Daniel C.","family":"Koboldt","sequence":"first","affiliation":[{"name":"The Genome Center at Washington University School of Medicine, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ken","family":"Chen","sequence":"additional","affiliation":[{"name":"The Genome Center at Washington University School of Medicine, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Todd","family":"Wylie","sequence":"additional","affiliation":[{"name":"The Genome Center at Washington University School of Medicine, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David E.","family":"Larson","sequence":"additional","affiliation":[{"name":"The Genome Center at Washington University School of Medicine, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael D.","family":"McLellan","sequence":"additional","affiliation":[{"name":"The Genome Center at Washington University School of Medicine, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elaine R.","family":"Mardis","sequence":"additional","affiliation":[{"name":"The Genome Center at Washington University School of Medicine, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George M.","family":"Weinstock","sequence":"additional","affiliation":[{"name":"The Genome Center at Washington University School of Medicine, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard K.","family":"Wilson","sequence":"additional","affiliation":[{"name":"The Genome Center at Washington University School of Medicine, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Ding","sequence":"additional","affiliation":[{"name":"The Genome Center at Washington University School of Medicine, St Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2009,6,19]]},"reference":[{"key":"2023013112101170200_B1","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/nature07517","article-title":"Accurate whole human genome sequencing using reversible terminator chemistry","volume":"456","author":"Bentley","year":"2008","journal-title":"Nature"},{"key":"2023013112101170200_B2","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1101\/gr.070227.107","article-title":"Quality scores and SNP detection in sequencing-by-synthesis systems","volume":"18","author":"Brockman","year":"2008","journal-title":"Genome Res."},{"key":"2023013112101170200_B3","doi-asserted-by":"crossref","first-page":"R32","DOI":"10.1186\/gb-2009-10-3-r32","article-title":"Evaluation of next generation sequencing platforms for population targeted sequencing studies","volume":"10","author":"Harismendy","year":"2009","journal-title":"Genome Biol"},{"key":"2023013112101170200_B4","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1038\/nmeth.1179","article-title":"Whole-genome sequencing and variant discovery in C. elegans","volume":"5","author":"Hillier","year":"2008","journal-title":"Nat Methods"},{"key":"2023013112101170200_B5","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1038\/ng.195","article-title":"High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi","volume":"40","author":"Holt","year":"2008","journal-title":"Nat. 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