Manual

• Introduction
  • Dependencies
  • Docker repos
• To use SomaticSeq.Wrapper.sh
  • To train data set into a classifier
  • To predict somatic mutation based on trained classifiers
  • To classify based on simple majority vote
• The step-by-step SomaticSeq Workflow
  • Combine the call sets
  • For model training: process and annotate the VCF files (union of call sets)
  • Convert the VCF file, annotated or otherwise, into a tab separated file
  • Model Training or Mutation Prediction
• To run the dockerized somatic mutation callers
  • Location
  • Requirements
  • Example commands
    • Parameters
    • What does the single-threaded command do
    • What does the multi-threaded command do
• Use BAMSurgeon to create training set
  • Requirements
• Release Notes
  • Version 1.0
  • Version 1.1
  • Version 1.2
  • Version 2.0
  • Version 2.0.2
  • Version 2.1.2
  • Version 2.2
  • Version 2.2.1
  • Version 2.2.2
  • Version 2.2.3
  • Version 2.2.4
  • Version 2.2.5
  • Version 2.3.0
  • Version 2.3.1
  • Version 2.3.2
  • Version 2.4.0
  • Version 2.4.1
  • Version 2.5.0
  • Version 2.5.1
  • Version 2.5.2
  • Version 2.6.0
  • Version 2.6.1
  • Version 2.7.0
  • Version 2.7.1
  • Version 2.7.2
  • Version 2.8.0
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