SomaticSniper is a software for comparing tumor and normal pairs. The developer estimate its sensitivity and precision, and present several common sources of error resulting in miscalls.
The Genome Institute at Washington University
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Bioinformatics. 2012 Feb 1;28(3):311-7.
SomaticSniper: Identification of Somatic Point Mutations in Whole Genome Sequencing Data.
Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, Ding L.