/CapSeg

CapSeg - Copy Number from Exome Sequencing
  1. R 83.2%
  2. Python 10.2%
  3. Scala 6.5%
  4. Perl 0.1%
R Python Scala Perl

Clone with HTTPS

Use Git or checkout with SVN using the web URL.

Download ZIP
Find file
Switch branches/tags
Nothing to show
Latest commit 6d1ec0f Sep 17, 2013 @aaronmck moving around the epsilon correction code
Permalink
Failed to load latest commit information.
R moving around the epsilon correction code Sep 17, 2013
inst first commit Sep 18, 2012
man first commit Sep 18, 2012
setup first commit Sep 18, 2012
utils cleaning up some of the parameters for tangent that plug through to C… Aug 3, 2013
DESCRIPTION
README.md basic formatting issues Jul 20, 2013
TODO.txt Create TODO.txt Feb 20, 2013

README.md

CapSeg

CapSeg - Copy number from exome sequencing

Aaron McKenna

CapSeg is a tool for transforming exome sequencing data to copy number information in cancer samples.
Using a toolkit based on the GATK, Queue, R, and python, CapSeg transforms input paired tumor-normal BAM files into segmented copy number calls.

Prerequisites installed on the machine are:

  • Java 1.6.anything; Java 1.7 is not yet supported
  • Python 2.7+ (Python 3.X is not yet supported)
  • R 3.0 or greater, including the following packages:
    • optparse
    • DNAcopy
    • plyr
    • corpcor
  • Samtools (any version should do)

Versions

v1.0

  • Initial commit

v1.0.1

  • Introduced seperate directories for input and output of the tangent planes (historical data)
  • Minor bug fixes