Contents

• About
  • Getting Help
  • Install Instructions
    • 1. Install Aligner
    • 2. Install MAVIS
      • Install using pip
      • Install using Buildout
    • 3. Build or Download Reference Files
  • Citation
• Inputs
  • Reference Input Files
    • Reference Genome
    • Template Metadata
    • Masking File
    • Annotations
      • Generating the Annotations from Ensembl
    • DGV (Database of Genomic Variants) Annotations
    • Aligner Reference
  • MAVIS standard input file format
    • Required Columns
    • Optional Columns
    • Summary by Pipeline Step
• Supported Dependencies
  • Job Schedulers
  • Aligners
  • SV Callers
    • DELLY Post-processing
    • Writing A Custom Conversion Script
      • Logic Example - Chimerascan
    • Calling A Custom Conversion Script
    • General VCF inputs
• Running the Pipeline
  • Running MAVIS using a Job Scheduler
    • Configuring Scheduler Settings
    • Troubleshooting Dependency Failures
  • MAVIS (Mini) Tutorial
  • MAVIS (Full) Tutorial
    • Getting the Tutorial Data
    • Downloading the Reference Inputs
    • Generating the Config File
    • Setting Up the Pipeline
    • Submitting Jobs to the Cluster
    • Analyzing the Output
• Configuration and Settings
  • Pipeline Configuration File
  • Environment Variables
  • Adjusting the Resource Requirements
    • Choosing the Number of Validation/Annotation Jobs
    • Uninformative Filter
• Resource Requirements
  • Validation Resources
  • Annotation Resources
• Theory and Models
  • Introduction
  • Evidence
    • Types of Flanking evidence
      • Deletion
      • Insertion
      • Duplication
      • Inversion
      • Translocation
      • Inverted Translocation
    • Compatible Flanking Pairs
    • Calculating the Evidence Window
    • Calling Breakpoints by Flanking Evidence
    • Determining Flanking support
  • Classifying Events
  • Assembling Contigs
  • Annotating Events
  • Predicting Splicing Patterns
  • Pairing Similar Events
    • Literature
• Illustrations
  • Fusion Diagrams
  • Transcript Overlays
• Guidelines for Contributors
  • Getting Started
  • Install (for Development)
  • Build the Sphinx Documentation
  • Deploy to PyPi
    • Reporting a Bug
    • Coding Conventions
      • Formatting/Style
        • Types in docstrings
      • Tests
  • Major Assumptions
  • Current Limitations
  • Computing Code coverage
• Package Documentation
  • align module
  • 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
    • fusion module
    • genomic module
    • main module
    • protein module
    • splicing 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
  • config 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
  • schedule subpackage
    • constants module
    • job module
    • local module
    • pipeline module
    • scheduler module
  • summary subpackage
    • Sub-package Documentation
      • Output Files
      • Algorithm Overview
    • constants module
    • main module
    • summary module
  • tools module
  • util module
• Glossary
  • General Terms
  • Configurable Settings
  • Column Names

Indices and tables

• Index

• Module Index

• Search Page