Welcome to Cancer Predisposition Sequencing Reporter’s documentation!

Table of Contents

• About
  • What is the Cancer Predisposition Sequencing Preporter (CPSR)?
  • Example report
  • Docker-based technology
  • Contact
• Getting started
  • STEP 0: Python
  • STEP 1: Installation of Docker
  • STEP 2: Download run script/data bundle, and pull Docker image
  • STEP 3: Input preprocessing
  • STEP 4: Configuration
  • STEP 5: 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)
• CHANGELOG