deepSNV

Detection of subclonal SNVs in deep sequencing experiments.

Bioconductor version: Release (2.12)

This package provides provides a quantitative variant caller for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. It assumes a comparative setup with a control experiment of the same loci and a beta-binomial model to discriminate sequencing errors and subclonal SNVs.

Author: Moritz Gerstung and Niko Beerenwinkel

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

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("deepSNV")

Documentation

PDF	R Script	An R package for detecting low frequency variants in deep sequencing experiments
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, GeneticVariability, Genetics, SNP, Sequencing, Software
Version	1.6.0
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
Imports	Rsamtools
Suggests
System Requirements
URL	http://www.cbg.ethz.ch/software/deepSNV
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source	deepSNV_1.6.0.tar.gz
Windows Binary	deepSNV_1.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	deepSNV_1.6.0.tgz
Package Downloads Report	Download Stats

Workflows »

Common Bioconductor workflows include:

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Hosting provided by Fred Hutchinson Cancer Research Center