Personal Cancer Genome Reporter
v0.6.2.1

Table of Contents

  • About
  • Getting started
  • Annotation resources
  • Input
  • Output
  • Tier models
  • CHANGELOG
Personal Cancer Genome Reporter
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  • Welcome to Personal Cancer Genome Reporter’s documentation!
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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
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© Copyright 2017/2018, Sigve Nakken Revision 306d6dda.

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