Department of Bioinformatics and Computational Biology

Publications:22155872

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

Bioinformatics 28 (3):311-7
Feb 2012

Larson D, Harris C, Chen K, Koboldt D, Abbott T, Dooling D, Ley T, Mardis E, Wilson R, Ding L

The Genome Institute, Washington University, St Louis, MO 63108, USA. delarson@wustl.edu

Abstract

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.