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

DE Larson, CC Harris, K Chen, DC Koboldt… - …, 2012 - academic.oup.com
DE Larson, CC Harris, K Chen, DC Koboldt, TE Abbott, DJ Dooling, TJ Ley, ER Mardis
Bioinformatics, 2012academic.oup.com
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 …
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.
Oxford University Press