vcfsim 1.0

What is vcfsim?

vcfsim is a command-line tool for generating simulated VCFs (Variant Call Format files used to encode genetic variation data). It pairs a coalescent simulation backend (msprime) with lightweight postprocessing to produce biologically realistic VCFs with parameterized missing data — a full simulated dataset can be created from just a few command-line arguments.

In particular, vcfsim makes it easy to simulate all-sites VCFs that contain both variant and invariant sites. All-sites VCFs are required for unbiased estimation of π and d_xy (see pixy), and are typically expensive to obtain from real data — vcfsim is designed to drop straight into pixy-style workflows for testing, benchmarking, and methods development.

vcfsim also supports two missing-data models (uniform and HMM-based spatial clustering), arbitrary ploidy, custom sample names, two-population splits, and multi-chromosome batch runs from a parameter file.

Documentation

• About vcfsim
  • Why simulated all-sites VCFs?
  • Notable features
  • Acknowledgements
• Installation
  • Via conda
  • From source
• Arguments
  • Required
  • In addition, one of (sample specification)
  • In addition, one of (missing-data model)
  • Optional (simulation parameters)
  • Optional (output)
  • Optional (multi-chromosome batch mode)
  • Optional (population structure)
  • Help
  • Example
• Changelog
  • Unreleased
    • Documentation
  • vcfsim 1.0.29
    • New features
    • Bug fixes
    • Packaging
• Contributing
  • Installing the development version
  • Project layout
  • Working on the documentation
  • Reporting bugs and requesting features
  • Pull request workflow
  • License

Guides

• Basic usage
  • A first run
  • Producing replicates
  • Custom sample names
  • Writing to stdout
• Missing data models
  • Uniform site missingness
  • HMM-based spatially clustered missingness
    • How the HMM works
    • Picking parameters
  • Mixing the two models
• Simulating a population split
  • The model
  • Sample distribution
  • Using the output for F_ST simulations
• Multi-chromosome runs
  • The parameter file format
  • Running with a parameter file
  • Combining with custom sample names

How should I cite vcfsim?

If you use vcfsim in your research, please cite the repository and the underlying coalescent simulator:

• vcfsim: https://github.com/samuk-lab/vcfsim

• Baumdicker, F. et al. (2022). Efficient ancestry and mutation simulation with msprime 1.0. Genetics, 220(3), iyab229. https://doi.org/10.1093/genetics/iyab229