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.
- About pixy
- Companion files
- Generating invariant sites VCFs
- Step by Step Installation and Usage
- Usage Examples
- Understanding pixy output
- Plotting pixy output
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).