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© 2016 John Wiley & Sons, Inc. CaVEMan is an expectation maximization-based somatic substitutiondetection algorithm that is written in C. The algorithm analyzes sequence data from a test sample, such as a tumor relative to a reference normal sample from the same patient and the reference genome. It performs a comparative analysis of the tumor and normal sample to derive a probabilistic estimate for putative somatic substitutions.When combined with a set of validated post-hoc filters, CaVEMan generates a set of somatic substitution calls with high recall and positive predictive value. Here we provide instructions for using a wrapper script called cgpCaVEManWrapper, which runs the CaVEMan algorithm and additional downstream post-hoc filters. We describe both a simple one-shot run of cgpCaVEManWrapper and a more in-depth implementation suited to large-scale compute farms.

Original publication

DOI

10.1002/cpbi.20

Type

Journal article

Journal

Current Protocols in Bioinformatics

Publication Date

01/01/2016

Volume

2016

Pages

15.10.1 - 15.10.18