cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data - PubMed (original) (raw)
cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data
David Jones et al. Curr Protoc Bioinformatics. 2016.
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.
Keywords: SNV; cancer; sequencing; somatic; substitution.
Copyright © 2016 John Wiley & Sons, Inc.
Figures
Figure 15.10.1
cgpCavEManWrapper workflow. If –
p/-i
options are omitted, individual componenets are automatically executed. On restart, the workflow will automatically recover to the last successful point if killed for any reason.
Figure 15.10.2
UCSC Table Browser settings for generation of the
centromeric_repeats.bed.gz
file.
Figure 15.10.3
UCSC Table Browser filter settings for generation of the
centromeric_repeats.bed.gz
file.
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