MAVIS User Manual

• About
• Getting started
  • Input Files
    • Required Columns
  • Reference Files
    • Reference Genome
    • Annotations
    • Template Metadata
    • Masking File
  • Running the Pipeline
  • Configuration and Settings
    • Generating a config file automatically
    • Manually creating the configuration File
    • Environment Variables
• Theory and Models
  • Types of Flanking evidence
    • Deletion
    • Insertion
    • Duplication
    • Inversion
    • Translocation
    • Inverted Translocation
  • Compatible Flanking Pairs
  • Calculating the Evidence Window
  • Classifying Events
  • Assembling Contigs
  • Calling Breakpoints by Flanking Evidence
  • Determining Flanking support
  • Annotating Events
  • Predicting Splicing Patterns
  • Pairing Similar Events
  • Glossary
• Development
  • Install
  • Non-python dependencies
    • Aligner (blat)
    • Samtools
  • Guidelines for Contributors
    • Formatting Types in docstrings
    • Unit Tests
    • Major Assumptions
    • Current Limitations
  • MAVIS Package Documentation
    • annotate subpackage
      • Sub-package Documentation
        • Types of Output Files
        • Algorithm Overview
        • Levels of Annotations
        • Overview of Class Relationships
      • base module
      • constants module
      • file_io module
      • genomic module
      • main module
      • protein module
      • variant module
    • assemble module
    • bam subpackage
      • cache module
      • cigar module
      • read module
      • stats module
    • blat module
    • breakpoint module
    • cluster subpackage
      • Sub-package Documentation
        • Types of Output Files
        • Algorithm Overview
      • cluster module
      • constants module
      • main module
    • constants module
    • error module
    • illustrate subpackage
      • constants module
      • diagram module
      • elements module
      • scatter module
      • util module
    • interval module
    • pairing subpackage
      • Sub-package Documentation
        • Output Files
        • Algorithm Overview
      • constants module
      • main module
      • pairing module
    • validate subpackage
      • Sub-package Documentation
        • Types of Output Files
        • Algorithm Overview
      • base module
      • call module
      • constants module
      • evidence module
      • main module
  • Development Goals

Indices and tables

• Index
• Module Index
• Search Page