cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data

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  • David Jones
    Cancer Genome Project, Wellcome Trust Sanger Institute Cambridge United Kingdom
  • Keiran M. Raine
    Cancer Genome Project, Wellcome Trust Sanger Institute Cambridge United Kingdom
  • Helen Davies
    Cancer Genome Project, Wellcome Trust Sanger Institute Cambridge United Kingdom
  • Patrick S. Tarpey
    Cancer Genome Project, Wellcome Trust Sanger Institute Cambridge United Kingdom
  • Adam P. Butler
    Cancer Genome Project, Wellcome Trust Sanger Institute Cambridge United Kingdom
  • Jon W. Teague
    Cancer Genome Project, Wellcome Trust Sanger Institute Cambridge United Kingdom
  • Serena Nik‐Zainal
    Cancer Genome Project, Wellcome Trust Sanger Institute Cambridge United Kingdom
  • Peter J. Campbell
    Cancer Genome Project, Wellcome Trust Sanger Institute Cambridge United Kingdom

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<jats:title>Abstract</jats:title><jats:p>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.</jats:p>

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