SomaticSniper: identification of somatic point mutations in whole genome sequencing data

被引：465

作者：

Larson, David E. ^{[1
,2
]}

Harris, Christopher C. ^{[1
]}

Chen, Ken ^{[1
,2
]}

Koboldt, Daniel C. ^{[1
]}

Abbott, Travis E. ^{[1
]}

Dooling, David J. ^{[1
,2
]}

Ley, Timothy J. ^{[1
,2
,3
,4
]}

Mardis, Elaine R. ^{[1
,2
,4
]}

Wilson, Richard K. ^{[1
,2
,4
]}

Ding, Li ^{[1
,2
]}

机构：

[1] Washington Univ, Genome Inst, St Louis, MO 63108 USA

[2] Washington Univ, Dept Genet, St Louis, MO 63108 USA

[3] Washington Univ, Dept Internal Med, Div Oncol, St Louis, MO 63108 USA

[4] Washington Univ, Siteman Canc Ctr, St Louis, MO 63108 USA

来源：

BIOINFORMATICS | 2012年 / 28卷 / 03期

关键词：

ACUTE MYELOID-LEUKEMIA; CANCER GENOME; CATALOG; ARID1A; TUMORS;

D O I：

10.1093/bioinformatics/btr665

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

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. 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. 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.

引用

页码：311 / 317

页数：7

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