deepSNV

Detection of subclonal SNVs in deep sequencing experiments.

Bioconductor version: Development (2.13)

This package provides provides a quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm assumes 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 prior knowledge, e.g. from variation data bases such as COSMIC and multiple samples for precisely estimating model parameters such as local error rates and dispersion.

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")

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