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

• Published in: Bioinformatics Vol. 28; no. 3; pp. 311 - 317
• Main Authors: Larson, David E., Harris, Christopher C., Chen, Ken, Koboldt, Daniel C., Abbott, Travis E., Dooling, David J., Ley, Timothy J., Mardis, Elaine R., Wilson, Richard K., Ding, Li
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.02.2012
• Subjects: Biological and medical sciences; Fundamental and applied biological sciences. Psychology; General aspects; Genome, Human; Humans; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Neoplasms - genetics; Original Papers; Point Mutation; Polymorphism, Single Nucleotide; Software; Somatic mutation; Data; Identification; Genome; Sequencing; Point mutation
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btr665

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.