deepSNV

Detection of subclonal SNVs in deep sequencing experiments.

Bioconductor version: Release (2.11)

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 1.4.0
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_1.4.0.tar.gz
Windows Binary deepSNV_1.4.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) deepSNV_1.4.0.tgz
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