Welcome to Cancer Predisposition Sequencing Reporter’s documentation!

Table of Contents

• About
  • What is the Cancer Predisposition Sequencing Reporter (CPSR)?
  • Example report
  • Docker-based technology
  • Contact
• Getting started
  • STEP 0: Python
  • STEP 1: Install PCGR (version 0.9.1)
  • STEP 2: Download the latest release
  • STEP 3: Configuration
  • STEP 4: Run example
• CPSR 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
  • Phenotype ontologies
• Input
  • VCF
  • CPSR configuration file
• Output
  • Interactive HTML report
  • Example report
  • JSON
  • Output files - germline SNVs/InDels
• Variant classification (ACMG/AMP)
• CHANGELOG
  • 0.6.1 - November 30th 2020
  • 0.6.0rc - September 24th 2020
  • 0.5.2 - November 18th 2019
  • 0.5.1 - October 14th 2019
  • 0.5.0 - September 23rd 2019