SomaticSniper: Identification of Somatic Point Mutations in Whole Genome Sequencing Data

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2011 Dec 14

PMID 22155872

Citations 369

Authors

David E Larson

Christopher C Harris

Ken Chen

Daniel C Koboldt

Travis E Abbott

David J Dooling

Timothy J Ley

Elaine R Mardis

Richard K Wilson

Li Ding

Affiliations

Soon will be listed here.

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.

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