Welcome to BASHer’s documentation!

Contents:

• BASHer (BiAllellic SNP Haplotyper)
  • What does this app do?
  • What are typical use cases for this script?
  • What inputs are required for this software to run?
  • How does this script work?
  • Known Limitations of this Software
    • Sex checking of embryos
    • Sample mixup
    • Recombination
    • Consanguinity
    • Telomeric & Centromeric Regions
• BASHer Usage
  • Command line usage
  • Running Basher via excel_parser.py helper script
    • Running excel_parser.py from the command line
    • Running excel_parser.py via a GUI
• Developer
  • Automated Testing Using Pytest
    • Unit Tests
    • Functional Tests
    • Coverage
    • Run Tests and Coverage
    • Debugging Tests
  • Sphinx Documentation
    • Editing Sphinx Documentation
    • Compiling Sphinx Documentation
  • Release Process
• Deployment
  • Get BASHer from GitHub Repo
  • Set Configuration via Config.py
  • Configure helper scripts, if used
    • Background
    • Configuring Helper Scripts
    • Test Deployment
• Internal BASHer Logic
  • Autosomal dominant logic
  • Autosomal recessive logic
  • X-linked logic
• Changelog

Indices and tables

• Index

• Module Index

• Search Page