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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v: v0.6.2.1
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