Welcome to Personal Cancer Genome Reporter’s documentation!

Table of Contents

• About
  • What is the Personal Cancer Genome Reporter (PCGR)?
  • Example reports
  • Why use PCGR?
  • Docker-based technology
  • Contact
• Getting started
  • STEP 0: Python
  • STEP 1: Installation of Docker
  • STEP 2: Download PCGR and data bundle
  • STEP 3: Input preprocessing
  • STEP 4: Configure PCGR
  • STEP 5: Run example
• Annotation resources
  • Basic variant consequence annotation
  • Insilico predictions of effect of coding variants
  • Variant frequency databases
  • Variant databases of clinical utility
  • Protein domains/functional features
  • Cancer gene knowledge bases
  • Pathway databases
  • Notes on variant annotation datasets
• Input
  • VCF
  • Copy number segments
  • PCGR configuration file
• Output
  • Interactive HTML report
  • JSON (beta)
  • Output files - somatic SNVs/InDels
  • Output files - somatic copy number aberrations
• Tier models
  • Tier model 1 - pcgr
  • Tier model 2 - pcgr_acmg
• CHANGELOG
  • 0.6.2.1 - May 14th 2018
  • 0.6.2 - May 9th 2018
  • 0.6.1 - May 2nd 2018
  • 0.6.0 - April 25th 2018