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 your PCGR workflow
  • STEP 5: Run example
• FAQ
• PCGR 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
  • Knowledge resources on gene and protein targets
  • Pathway databases
  • Notes on variant annotation datasets
• Input
  • VCF
  • Copy number segments
  • PCGR configuration file
• Output
  • Interactive HTML report (flexdashboard)
  • Interactive HTML report (rmarkdown)
  • JSON
  • Output files - somatic SNVs/InDels
  • Output files - somatic copy number aberrations
• Tier models
  • pcgr_acmg
• CHANGELOG
  • 0.9.1 - November 30th 2020
  • 0.9.0rc - September 24th 2020
  • 0.8.4 - November 18th 2019
  • 0.8.3 - October 14th 2019
  • 0.8.2 - Sep 29th 2019
  • 0.8.1 - May 22nd 2019
  • 0.8.0 - May 20th 2019
  • 0.7.0 - Nov 27th 2018
  • 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