MoCha Oncogenic MOI Annotator (MOMA)
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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
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4. Technical Details
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4. Technical Details
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