deepSNV

An R package for calling subclonal single-nucleotide variants from paired deep sequencing experiments.

Current version

1.2.3 Apr 2012

Description

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.

Installation

deepSNV is distributed under the GNU General Public License.

The source package has been tested on Mac and Linux, binary versions for Mac and Windows are also available.

Bioconcoductor

The latest version is available on bioconductor package requires R >= 2.15 and bioconducor 2.10. This is the preferred way of installing deepSNV. You can install the package via

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

> biocLite("deepSNV")

Older versions

This site hosts an older version of deepSNV (0.99.3) that can be manually installed. It  requires R >= 2.13 and the VGAM package that can be installed from CRAN with the

> install.packages("VGAM")

command, and Rsamtools which can be installed from Bioconductor via

> source("http://www.bioconductor.org/biocLite.R"); biocLite("Rsamtools")

You can install the actual package with

> install.packages("deepSNV", repos="http://www.cbg.ethz.ch/software/deepSNV")

And you are done.

Additional Information

After installation you can load the package with

> library(deepSNV)

and use the R help

> ?deepSNV

Additional examples can be found in the vignette:

> vignette("deepSNV")

Authors and Contributors

• Moritz Gerstung
• Niko Beerenwinkel

Citations

When using deepSNV, please cite:

Gerstung, M., Beisel, C., Rechsteiner, M., Wild, P., Schraml, P., Moch, H., and Beerenwinkel, N. (2012). Reliable detection of subclonal single-nucleotide variants in tumor cell populations. Nat Commun, 3:811, doi: 10.1038/ncomms1814.

Contact

Moritz Gerstung