MoCha Oncogenic MOI Annotator (MOMA)
latest
  • 1. Introduction
    • 1.1. MOMA Workflow
  • 2. Installation
    • 2.1. Requirements
      • 2.1.1. Scripting Languages
      • 2.1.2. Annovar Variant Annotation Package
        • 2.1.2.1. Annovar Package Installation
        • 2.1.2.2. Annovar Database Installation
        • 2.1.2.3. Human Reference hg19
    • 2.2. Setting up MOMA
    • 2.3. Running Tests
  • 3. Running MOMA
    • 3.1. Basic Usage
      • 3.1.1. Required Arguments
        • 3.1.1.1. Data Source Argument
        • 3.1.1.2. MOMA Input Files (Data File Argument)
      • 3.1.2. Optional Arguemnts
        • 3.1.2.1. Output and Formatting
        • 3.1.2.2. CNV Output Arguments
        • 3.1.2.3. Fusion Output Argument
        • 3.1.2.4. Filtering Arguments
    • 3.2. Variant Type Inputs and Processing
      • 3.2.1. SNV / Indel (small variants) Processing
      • 3.2.2. CNV Processing
      • 3.2.3. Fusion Processing
    • 3.3. MOMA Output
      • 3.3.1. SBS-6 Output
    • 3.4. MOMA Logging
      • 3.4.1. Variant Counts and MOI Counts Tables
    • 3.5. Troubleshooting
      • 3.5.1. Missing or Unexpected Variants
        • 3.5.1.1. Case 1: Missing TP53 Variant from MOMA Report
      • 3.5.2. Pipeline Errors
      • 3.5.3. Other Troubleshooting Strategies
        • 3.5.3.1. Verbose Logging
        • 3.5.3.2. Keep All Output
      • 3.5.4. Summary
  • 4. Technical Details
Index Search
MoCha Oncogenic MOI Annotator (MOMA)
  • Docs »
  • Search
  • Edit on GitHub

© Copyright 2020, Dave Sims Revision 6ec4359a.

Built with Sphinx using a theme provided by Read the Docs.