pixy 1.2.7.beta1

What is pixy?

pixy is a command line tool for calculating the population genetic summary statistics pi (average per site heterozygosity) and dxy (average number of nucleotide differences between populations per site) from a VCF file.

Many tools for computing pi and dxy from VCFs produce biased estimates in the presence of missing data. This is because these methods often make the simplifying assumption that if a genotype is missing, it is homozygous reference (0/0) by state. See pixy’s paper (https://doi.org/10.1111/1755-0998.13326) for more details.

Documentation

• About pixy
  • pixy avoids common pitfalls in computing pi and dxy
  • Notable features of pixy
• Installation
  • Via Anaconda
  • Via Git or Download
• Arguments
  • Required:
  • In addition, one of either:
  • Optional arguments:
• Companion files
  • Populations file
  • BED file
  • Sites file
• Changelog
  • 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 Anaconda
  • 3. Create a New Environment
  • 4. Install pixy
  • 5. Create a populations file
  • 6. Compress and Index your VCF
  • 7. Run pixy
  • 8. Profit
  • 9. Stay up to date
• Usage Examples
  • Basic usage
  • Focusing on a specific genomic interval
  • Using a .BED file to define windows
  • Using a sites file to limit calculations to specific sites
  • Site-level estimates
• Understanding pixy output
  • Output file contents
    • Within population nucleotide diversity (pi)
    • Between population nucleotide divergence (dxy)
    • Weir and Cockerham’s FST (fst)
  • Working with pixy output data
    • Plotting results
    • 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

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).