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Documentation

  • About
    • Why population count masks?
    • Input modes
      • BAM/CRAM mode
      • All-sites VCF mode
    • Sparse output
  • Installation
    • Requirements
    • Conda environment
    • Verify the CLI
    • Build these docs locally
  • Arguments
    • Commands
    • Core arguments
    • Input-specific arguments
    • Shared optional arguments
    • BAM/CRAM mode options
    • Examples
  • Input files
    • Sample table for BAM/CRAM mode
    • Popfile for all-sites VCF mode
    • Sample and population labels
    • All-sites VCF
    • Variants-only VCF for BAM/CRAM mode
      • Threshold estimation
      • Variant exclusions
    • Mask BED
  • Examples
    • BAM/CRAM smoke run
    • Keep intermediate files
    • BAM/CRAM with a variants-only VCF
    • All-sites VCF run
    • Query the output
    • Overwrite existing outputs
  • Output files
    • Final outputs
    • BED columns
    • Metadata
    • Sparse interpretation
    • Intermediate files

Reference

  • Development
    • Set up a development environment
    • Run checks
    • Build documentation
    • Project layout
    • Implementation overview
  • API Reference
    • Configuration
      • AlignmentRunConfig
      • VcfRunConfig
    • Workflow
    • Samples
      • read_popfile()
      • read_samples()
    • Output summaries
  • Changelog
    • 0.1.0
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