source("http://bioconductor.org/biocLite.R")
biocLite("deepSNV")

deepSNV

Detection of subclonal SNVs in deep sequencing experiments.

Bioconductor version: 2.13

This package provides provides a 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 new shearwater algorithm (beta) 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: Moritz Gerstung and Niko Beerenwinkel

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

Installation

To install this package, start R and enter:

source("http://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
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, GeneticVariability, Genetics, SNP, Sequencing, Software
Version	1.8.0
In Bioconductor since	BioC 2.10 (R-2.15)
License	GPL-3
Depends	R (>= 2.13.0), Rsamtools(>= 1.4.3), GenomicRanges, IRanges, Biostrings, VGAM, methods, graphics, VariantAnnotation(>= 1.5.0), parallel
Imports	Rsamtools
Suggests	RColorBrewer, knitr
System Requirements
URL	http://www.cbg.ethz.ch/software/deepSNV
Depends On Me
Imports Me
Suggests Me	h5vc

Package Archives

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

Package Source	deepSNV_1.8.0.tar.gz
Windows Binary	deepSNV_1.8.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	deepSNV_1.8.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats