deepSNV

DOI: 10.18129/B9.bioc.deepSNV    

Detection of subclonal SNVs in deep sequencing data.

Bioconductor version: Release (3.8)

This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes classifier based on a beta-binomial model for variant calling with multiple samples for precisely estimating model parameters - such as local error rates and dispersion - and prior knowledge, e.g. from variation data bases such as COSMIC.

Author: Niko Beerenwinkel [ths], David Jones [ctb], Inigo Martincorena [ctb], Moritz Gerstung [aut, cre]

Maintainer: Moritz Gerstung <moritz.gerstung at ebi.ac.uk>

Citation (from within R, enter citation("deepSNV")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("deepSNV", version = "3.8")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("deepSNV")

 

PDF R Script An R package for detecting low frequency variants in deep sequencing experiments
HTML R Script Shearwater ML
PDF R Script Subclonal variant calling with multiple samples and prior knowledge using shearwater
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, GeneticVariability, Genetics, SNP, Sequencing, Software
Version 1.28.0
In Bioconductor since BioC 2.10 (R-2.15) (6.5 years)
License GPL-3
Depends R (>= 2.13.0), methods, graphics, parallel, Rhtslib, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation(>= 1.13.44)
Imports Rhtslib
LinkingTo Rhtslib(>= 1.13.1)
Suggests RColorBrewer, knitr, rmarkdown
SystemRequirements
Enhances
URL http://github.com/gerstung-lab/deepSNV
Depends On Me
Imports Me
Suggests Me GenomicFiles
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package deepSNV_1.28.0.tar.gz
Windows Binary deepSNV_1.28.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) deepSNV_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/deepSNV
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/deepSNV
Package Short Url http://bioconductor.org/packages/deepSNV/
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