CgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data. Issue 1 (8th December 2016)

• Record Type: Journal Article
• Authors: Jones, David; Raine, Keiran M.; Davies, Helen; Tarpey, Patrick S.; Butler, Adam P.; Teague, Jon W.; Nik‐Zainal, Serena; Campbell, Peter J.
• Editors: Bateman, Alex; Pearson, William R.; Stein, Lincoln D.; Stormo, Gary D.; Yates, John R.
• Is Part Of: Current protocols in bioinformatics. Volume 56:Issue 1(2016)
• Page Start: 15.10.1
• Page End: 15.10.18
• Publication Date: 2016-12-08
• Subjects: somatic -- cancer -- sequencing -- SNV -- substitution; Bioinformatics -- Laboratory manuals; Nucleotide sequence -- Laboratory manuals; Amino acid sequence -- Laboratory manuals; Base Sequence; Amino Acid Sequence; Computational Biology -- methods; Databases, Genetic; Proteins -- analysis; Sequence Analysis -- methods; Sequence Homology; Amino acid sequence; Bioinformatics; Nucleotide sequence; Laboratory Manuals; Laboratory manuals; 570.285
• DOI: 10.1002/cpbi.20
• Languages: English
• ISSNs: 1934-3396

Abstract

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.