deepSNV

DOI: 10.18129/B9.bioc.deepSNV    

Detection of subclonal SNVs in deep sequencing data.

Bioconductor version: Release (3.6)

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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("deepSNV")

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
PDF	R Script	Subclonal variant calling with multiple samples and prior knowledge using shearwater
HTML	R Script	Shearwater ML
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, GeneticVariability, Genetics, SNP, Sequencing, Software
Version	1.24.0
In Bioconductor since	BioC 2.10 (R-2.15) (6 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
Suggests	RColorBrewer, knitr, rmarkdown
SystemRequirements
Enhances
URL	http://github.com/gerstung-lab/deepSNV
Depends On Me
Imports Me
Suggests Me	GenomicFiles
Build Report

Package Archives

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

Source Package	deepSNV_1.24.0.tar.gz
Windows Binary	deepSNV_1.24.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	deepSNV_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/deepSNV
Package Short Url	http://bioconductor.org/packages/deepSNV/
Package Downloads Report	Download Stats