SomaticSniper: identification of somatic point mutations in whole genome sequencing data
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...
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Published in | Bioinformatics Vol. 28; no. 3; pp. 311 - 317 |
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Main Authors | , , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
Oxford
Oxford University Press
01.02.2012
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Subjects | |
Online Access | Get full text |
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Summary: | 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.
Contact:
delarson@wustl.edu; lding@wustl.edu
Supplementary information:
Supplementary data are available at Bioinformatics online. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Associate Editor: Alex Bateman |
ISSN: | 1367-4803 1460-2059 1367-4811 |
DOI: | 10.1093/bioinformatics/btr665 |