cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data.
cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data.
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DOI：
10.1002/cpbi.20
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发表时间：
2016-12-08
影响因子：
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通讯作者：
Campbell, Peter J
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文献类型：
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作者：
Jones, David;Raine, Keiran M;Campbell, Peter J
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.
