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Authors:
Anna Fowler, Elise Ruark, Nazneen Rahman, Gerton Lunter
Description:
DECoN identifies deletion/duplications of whole exons in targeted sequencing data, and is most suitable for use on data generated in batches. It provides quality checks and visualisation to make it suitable for clinical use. It is implemented in R, but has a strict version control using packrat, and therefore will not be affected by future changes to any packages or their dependencies. It takes as input:
  • a set of BAM files
  • a BED file
  • a reference FASTA file
  • an optional file detailing clinical exon numbering of the BED file

And returns:

  • a list of failed samples and exons
  • a table of whole exon deletion/duplication in the samples
  • a summary file for use with the GUI

DECoN was created as part of the Mainstreaming Cancer Genetics programme.

Reference:
The manuscript is in preparation, please cite this website: Detection of Exon Copy Number: DECoN; A. Fowler, E. Ruark, N. Rahman, G. Lunter, www.well.ox.ac.uk/decon.
Resources:
Software registration and download
Documentation:  A user guide is provided with the download
Dependencies:
  • R v.3.1.2 or later

  • The capacity to build R packages from source; Rtools for windows or gcc and gfortran compilers for Mac OS X/Linux
  • The interactive GUI requires a modern internet browser, such as  Firefox, Chrome, OR IE (v.10 or later).
  • An Internet connection is required for setup.

Detailed instructions for downloading R and Rtools for Windows are provided with the download.

Installation:
Unpack the tarball to a local directory. In Mac OS X/Linux, run setup.sh from the local file. In Windows, click the setup.bat file.
Running DECoN: There are 4 sequential steps in a DECoN run: reading the BAM files, running quality checks, making deletion/duplication calls and then visualising the calls. After each step, a summary .RData file is created. This file is required for the next step.
 This allows the user to re-run individual steps without having to re-run previous steps.

An example workflow for Linux/Mac:

Rscript ReadInBams.R --bams bams.file --bed bed.file --fasta fasta.file --out output.bams

Rscript IdentifyFailures.R --Rdata output.bams.Rdata --out output.fails

Rscript makeCNVcalls.R --Rdata output.bams.Rdata --out output.calls Rscript runShiny.R --Rdata output.calls

A similar workflow can be executed in Windows by clicking the executables and entering the options when prompted.

Contact: Please submit all bug reports, comments, feature requests and other feedback to the DECoN User Group