snputils

snputils is a Python library for processing genetic variation, ancestry, phenotype, and relatedness data. It focuses on fast file I/O, ergonomic data containers, population-genetic statistics, dimensionality reduction, and visualization workflows for genomic analyses.

Install

Set up the package, optional extras, and local documentation build.

Installation

Quickstart

Load SNP, ancestry, phenotype, and IBD files with the high-level API.

Quickstart

Tutorials

Rendered notebooks for SNP objects, PCA, allele frequency, local ancestry, admixture mapping, and GRG workflows.

Tutorials

API Reference

Browse objects, readers, writers, analysis classes, statistics, datasets, and visualization functions by topic.

API Reference

Citation

If you use snputils in your research, please cite our paper:

@article{snputils2026,
  author = {Bonet, David and Comajoan Cara, Marçal and Barrabés, Míriam and Smeriglio, Riccardo and Agrawal, Devang and Aounallah, Khaled and Geleta, Margarita and Dominguez Mantes, Albert and Thomassin, Christophe and Shanks, Cole and Huang, Edward C. and Franquesa Monés, Marc and Luis, Aina and Saurina, Joan and Perera, Maria and López, Cayetana and Sabat, Benet Oriol and Abante, Jordi and Moreno-Grau, Sonia and Mas Montserrat, Daniel and Ioannidis, Alexander G.},
  title = {{snputils}: A High-Performance {Python} Library for Genetic Variation and Population Structure},
  year = {2026},
  month = feb,
  doi = {10.64898/2026.02.28.708618},
  url = {https://www.biorxiv.org/content/10.64898/2026.02.28.708618},
  journal = {bioRxiv},
  publisher = {Cold Spring Harbor Laboratory},
}