MAVIS User Manual

• About
  • Getting started
  • Non-python dependencies
    • Aligner
    • Samtools
• Running the Pipeline
  • Getting Help
  • Running MAVIS using a Job Scheduler
    • Standard
    • Non-Standard
    • Configuring Scheduler Settings
• MAVIS standard input file format
  • Required Columns
  • Optional Columns
  • Summary by Pipeline Step
• Reference Input Files
  • Reference Genome
  • Template Metadata
  • Masking File
  • Annotations
    • Generating the Annotations from Ensembl
  • DGV (Database of Genomic Variants) Annotations
  • Aligner Reference
• Configuration and Settings
  • Pipeline Configuration File
  • Environment Variables
• Supported SV Callers
  • DELLY Post-processing
  • Writing A Custom Conversion Script
    • Logic Example - Chimerascan
    • Calling A Custom Conversion Script
• Illustrations
  • Fusion Diagrams
  • Transcript Overlays
• Frequently Asked Questions
  • How can I use an unsupported tool?
  • How can I track my SV calls?
  • How to build the reference annotations input file?
  • Can I run mavis locally?
  • Why Does My Event Have 0 Spanning Reads?
  • I See Split Reads in IGV, Why Does MAVIS Call 0 Split Reads?
  • Why is the Breakpoint Called by MAVIS Different From What I See in IGV?
• 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
• Guidelines for Contributors
  • Install for Development
  • Formatting
    • Types in docstrings
  • Unit Tests
  • Major Assumptions
  • Current Limitations
  • Development Goals
• 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
  • checker 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
  • submit 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
• Literature

Indices and tables

• Index
• Module Index
• Search Page