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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

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