pixy 2.0.0.beta14

What is pixy?

pixy is a command-line tool for painlessly computing unbiased estimators of population genetic summary statistics that measure genetic variation within (π, θ_W, Tajima's D) and between (d_xy, F_ST) populations from a VCF.

Many tools for computing these summary statistics from VCFs produce biased estimates in the presence of missing data. This is because they often make the simplifying assumption that if a genotype is missing, it is homozygous reference (0/0) by state. See the pixy paper and the Watterson's θ / Tajima's D follow-up paper for the details.

As of version 2.0, pixy also supports organisms of arbitrary (and variable) ploidy, multiallelic sites, and both .tbi and .csi VCF indexes.

Documentation

• About pixy
  • pixy avoids common pitfalls in computing pi and dxy
  • Notable features of pixy
• Installation
  • Via conda
  • From source
• Arguments
  • Required
  • In addition, one of
  • Optional
  • Example
• Companion files
  • Populations file
  • BED file
  • Sites file
• Contributing
  • Prerequisites
  • Installing the development version
  • Project layout
  • Primary development commands
  • Shortcut task commands
  • Working on the documentation
  • Code style
  • Continuous integration
  • Reporting bugs and requesting features
  • Pull request workflow
  • Commit messages
  • Code of conduct
  • License
  • Release process (for maintainers)
• Changelog
  • pixy 2.0.0
    • New features
    • Bug fixes
    • Project / packaging
  • pixy 1.0.0
    • Summary of major changes
    • Detailed changelog
      • Major changes
      • New features
      • Removed features
      • Minor updates
      • Other bugfixes

Guides

• Generating invariant sites VCFs
  • Generating AllSites VCFs using BCFtools (mpileup/call)
  • Generating AllSites VCFs using GATK
• Step by Step Installation and Usage
  • 1. Generate a VCF with Invariant Sites and perform filtering
    • Site-level filtration
    • Optional: Population genetic filters
  • 2. Install a conda distribution
  • 3. Create a New Environment
  • 4. Install pixy
  • 5. Create a populations file
  • 6. Compress and Index your VCF
  • 7. Run pixy
  • 8. Interpret your results
  • 9. Stay up to date
• Usage Examples
  • Basic usage
  • Including the new 2.0 statistics
  • Focusing on a specific genomic interval
  • Using a .BED file to define windows
  • Using a sites file to limit calculations to specific sites
  • Including multiallelic SNPs
  • Switching the F_ST estimator
  • Site-level estimates
• Example data
  • Download
  • How the data were generated
  • Running pixy on the example
    • Expected results
    • Variants of the same data
• Understanding pixy output
  • Output file contents
    • Within-population nucleotide diversity (pi)
    • Between-population nucleotide divergence (dxy)
    • F_ST (fst)
    • Watterson's θ (watterson_theta)
    • Tajima's D (tajima_d)
  • Working with pixy output data
    • Post-hoc aggregating
• Plotting pixy output
  • Converting pixy output files to long format
  • Single chromosome view
  • A genome-wide plot of summary statistics

How should I cite pixy?

If you use pixy in your research, please cite the manuscript below, as well the Zenodo DOI of specific version of pixy used for your project.

Manuscript: Korunes, K.L. and Samuk, K. (2021), pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data. Molecular Ecology Resources. Accepted Author Manuscript. https://doi.org/10.1111/1755-0998.13326

And, if using the unbiased estimator of Tajima's D or Watterson's theta:

Bailey, N., Stevison, L., & Samuk, K. (2025). Correcting for bias in estimates of θw and Tajima’s D from missing data in next-generation sequencing. Molecular Ecology Resources, e14104. https://doi.org/10.1111/1755-0998.14104

Zenodo DOI for various versions of pixy: Go to https://zenodo.org/record/4432294 and find the DOI that matches the version used (the current version is shown first).