Welcome to Platypus 0.1.5 documentation!

Contents:

• 1. Introduction
• 2. Installation
  • 2.1. Dependencies
• 3. Running Platypus
• 4. Command Line Options
  • 4.1. Basic options
  • 4.2. BAM Data processing and filtering options
  • 4.3. Variant calling options
  • 4.4. Variant filtering options
  • 4.5. Miscellaneous options
  • 4.6. Deprecated command-line options
  • 4.7. Specifying calling regions
• 5. Description of Variant Calling Algorithm
  • 5.1. Read processing
  • 5.2. Construction of candidate variants
  • 5.3. Windowing
  • 5.4. Haplotype generation
  • 5.5. Calculation of haplotype likelihoods
  • 5.6. Estimation of haplotype frequencies
  • 5.7. Calling variants and genotypes
  • 5.8. Filtering

Indices and tables

• Index
• Module Index
• Search Page