title: cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data.
abstract: CaVEMan is an expectation maximization-based somatic substitution-detection 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. © 2016 by John Wiley & Sons, Inc.
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: David
authors.initials: D
authors.lastname: Jones
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Keiran M
authors.initials: KM
authors.lastname: Raine
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Helen
authors.initials: H
authors.lastname: Davies
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Tarpey
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Adam P
authors.initials: AP
authors.lastname: Butler
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Jon W
authors.initials: JW
authors.lastname: Teague
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Serena
authors.initials: S
authors.lastname: Nik-Zainal
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Campbell
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D014644:Genetic Variation / Q000235:genetics; D016678:Genome; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012984:Software
keywords: SNV; cancer; sequencing; somatic; substitution