/CapSeg

CapSeg - Copy Number from Exome Sequencing

Primary LanguageR

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