deepSNV

DOI: 10.18129/B9.bioc.deepSNV  

Detection of subclonal SNVs in deep sequencing data.

Bioconductor version: Release (3.17)

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], Raul Alcantara [ctb], David Jones [ctb], John Marshall [ctb], Inigo Martincorena [ctb], Moritz Gerstung [aut, cre]

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

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("deepSNV")

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	1.46.0
In Bioconductor since	BioC 2.10 (R-2.15) (11.5 years)
License	GPL-3
Depends	R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation(>= 1.27.6)
Imports	Rhtslib
LinkingTo	Rhtslib(>= 1.13.1)
Suggests	RColorBrewer, knitr, rmarkdown
SystemRequirements	GNU make
Enhances
URL
Depends On Me
Imports Me	mitoClone2
Suggests Me	GenomicFiles
Links To Me
Build Report

Package Archives

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

Source Package	deepSNV_1.46.0.tar.gz
Windows Binary	deepSNV_1.46.0.zip
macOS Binary (x86_64)	deepSNV_1.46.0.tgz
macOS Binary (arm64)	deepSNV_1.46.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/deepSNV
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/deepSNV
Bioc Package Browser	https://code.bioconductor.org/browse/deepSNV/
Package Short Url	https://bioconductor.org/packages/deepSNV/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive