VarScan: variant detection in massively parallel sequencing of individual and pooled samples

被引：966

作者：

Koboldt, Daniel C. ^{[1
]}

Chen, Ken ^{[1
]}

Wylie, Todd ^{[1
]}

Larson, David E. ^{[1
]}

McLellan, Michael D. ^{[1
]}

Mardis, Elaine R. ^{[1
]}

Weinstock, George M. ^{[1
]}

Wilson, Richard K. ^{[1
]}

Ding, Li ^{[1
]}

机构：

[1] Washington Univ, Sch Med, Genome Ctr, St Louis, MO 63108 USA

来源：

BIOINFORMATICS | 2009年 / 25卷 / 17期

关键词：

HUMAN GENOME;

D O I：

10.1093/bioinformatics/btp373

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 lenghts 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.

引用

页码：2283 / 2285

页数：3

共 11 条

[1] Accurate whole human genome sequencing using reversible terminator chemistry [J].

Bentley, David R. ;

Balasubramanian, Shankar ;

Swerdlow, Harold P. ;

Smith, Geoffrey P. ;

Milton, John ;

Brown, Clive G. ;

Hall, Kevin P. ;

Evers, Dirk J. ;

Barnes, Colin L. ;

Bignell, Helen R. ;

Boutell, Jonathan M. ;

Bryant, Jason ;

Carter, Richard J. ;

Cheetham, R. Keira ;

Cox, Anthony J. ;

Ellis, Darren J. ;

Flatbush, Michael R. ;

Gormley, Niall A. ;

Humphray, Sean J. ;

Irving, Leslie J. ;

Karbelashvili, Mirian S. ;

Kirk, Scott M. ;

Li, Heng ;

Liu, Xiaohai ;

Maisinger, Klaus S. ;

Murray, Lisa J. ;

Obradovic, Bojan ;

Ost, Tobias ;

Parkinson, Michael L. ;

Pratt, Mark R. ;

Rasolonjatovo, Isabelle M. J. ;

Reed, Mark T. ;

Rigatti, Roberto ;

Rodighiero, Chiara ;

Ross, Mark T. ;

Sabot, Andrea ;

Sankar, Subramanian V. ;

Scally, Aylwyn ;

Schroth, Gary P. ;

Smith, Mark E. ;

Smith, Vincent P. ;

Spiridou, Anastassia ;

Torrance, Peta E. ;

Tzonev, Svilen S. ;

Vermaas, Eric H. ;

Walter, Klaudia ;

Wu, Xiaolin ;

Zhang, Lu ;

Alam, Mohammed D. ;

Anastasi, Carole .

NATURE, 2008, 456 (7218) :53-59

[2] Quality scores and SNP detection in sequencing-by-synthesis systems [J].

Brockman, William ;

Alvarez, Pablo ;

Young, Sarah ;

Garber, Manuel ;

Giannoukos, Georgia ;

Lee, William L. ;

Russ, Carsten ;

Lander, Eric S. ;

Nusbaum, Chad ;

Jaffe, David B. .

GENOME RESEARCH, 2008, 18 (05) :763-770

[3] Evaluation of next generation sequencing platforms for population targeted sequencing studies [J].

Harismendy, Olivier ;

Ng, Pauline C. ;

Strausberg, Robert L. ;

Wang, Xiaoyun ;

Stockwell, Timothy B. ;

Beeson, Karen Y. ;

Schork, Nicholas J. ;

Murray, Sarah S. ;

Topol, Eric J. ;

Levy, Samuel ;

Frazer, Kelly A. .

GENOME BIOLOGY, 2009, 10 (03)

[4] Whole-genome sequencing and variant discovery in C-elegans [J].

Hillier, LaDeana W. ;

Marth, Gabor T. ;

Quinlan, Aaron R. ;

Dooling, David ;

Fewell, Ginger ;

Barnett, Derek ;

Fox, Paul ;

Glasscock, Jarret I. ;

Hickenbotham, Matthew ;

Huang, Weichun ;

Magrini, Vincent J. ;

Richt, Ryan J. ;

Sander, Sacha N. ;

Stewart, Donald A. ;

Stromberg, Michael ;

Tsung, Eric F. ;

Wylie, Todd ;

Schedl, Tim ;

Wilson, Richard K. ;

Mardis, Elaine R. .

NATURE METHODS, 2008, 5 (02) :183-188

[5] High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi [J].

Holt, Kathryn E. ;

Parkhill, Julian ;

Mazzoni, Camila J. ;

Roumagnac, Philippe ;

Weill, Francois-Xavier ;

Goodhead, Ian ;

Rance, Richard ;

Baker, Stephen ;

Maskell, Duncan J. ;

Wain, John ;

Dolecek, Christiane ;

Achtman, Mark ;

Dougan, Gordon .

NATURE GENETICS, 2008, 40 (08) :987-993

[6] Ultrafast and memory-efficient alignment of short DNA sequences to the human genome [J].

Langmead, Ben ;

Trapnell, Cole ;

Pop, Mihai ;

Salzberg, Steven L. .

GENOME BIOLOGY, 2009, 10 (03)

[7] The first human acute myeloid leukemia genome ever fully sequenced [J].

Falini, Brunangelo .

HAEMATOLOGICA, 2024, 109 (01) :1-2

[8] Mapping short DNA sequencing reads and calling variants using mapping quality scores [J].

Li, Heng ;

Ruan, Jue ;

Durbin, Richard .

GENOME RESEARCH, 2008, 18 (11) :1851-1858

[9] Sequencing of natural strains of Arabidopsis thaliana with short reads [J].

Ossowski, Stephan ;

Schneeberger, Korbinian ;

Clark, Richard M. ;

Lanz, Christa ;

Warthmann, Norman ;

Weigel, Detlef .

GENOME RESEARCH, 2008, 18 (12) :2024-2033

[10] The diploid genome sequence of an Asian individual [J].

Wang, Jun ;

Wang, Wei ;

Li, Ruiqiang ;

Li, Yingrui ;

Tian, Geng ;

Goodman, Laurie ;

Fan, Wei ;

Zhang, Junqing ;

Li, Jun ;

Zhang, Juanbin ;

Guo, Yiran ;

Feng, Binxiao ;

Li, Heng ;

Lu, Yao ;

Fang, Xiaodong ;

Liang, Huiqing ;

Du, Zhenglin ;

Li, Dong ;

Zhao, Yiqing ;

Hu, Yujie ;

Yang, Zhenzhen ;

Zheng, Hancheng ;

Hellmann, Ines ;

Inouye, Michael ;

Pool, John ;

Yi, Xin ;

Zhao, Jing ;

Duan, Jinjie ;

Zhou, Yan ;

Qin, Junjie ;

Ma, Lijia ;

Li, Guoqing ;

Yang, Zhentao ;

Zhang, Guojie ;

Yang, Bin ;

Yu, Chang ;

Liang, Fang ;

Li, Wenjie ;

Li, Shaochuan ;

Li, Dawei ;

Ni, Peixiang ;

Ruan, Jue ;

Li, Qibin ;

Zhu, Hongmei ;

Liu, Dongyuan ;

Lu, Zhike ;

Li, Ning ;

Guo, Guangwu ;

Zhang, Jianguo ;

Ye, Jia .

NATURE, 2008, 456 (7218) :60-U1

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