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