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arvkevi/ezancestry

Python tool that predicts a person's genetic ancestry from direct-to-consumer SNP data by comparing it against 1000 Genomes samples.

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What is it?

ezancestry predicts genetic ancestry from raw direct-to-consumer genetic files such as 23andMe and ancestry.com output, as well as VCF files. It places a user's genotypes alongside more than 2,500 samples from the 1000 Genomes Project and uses a k-nearest neighbors classifier trained on ancestry-informative SNPs (AISNPs) to assign continental and regional population labels.

The package ships with pretrained models for two published AISNP panels: a 55-SNP set from Kidd et al. and a 128-SNP set from Kosoy et al. (Seldin lab). Predictions can be made at the superpopulation or population level, with optional PCA-based dimensionality reduction.

A command-line interface provides fetch, predict, plot and train commands, and a Python API is available. Users can also supply a custom list of AISNPs and train new models to evaluate how well that panel separates ancestry groups, with cross-validation reports. A Streamlit app and a 3D scatter plot are provided for visualization.

Key features

  • 01Predicts ancestry from 23andMe, ancestry.com and VCF files
  • 02Compares user samples against 2,500+ 1000 Genomes samples
  • 03Ships pretrained k-NN models for Kidd (55 SNPs) and Seldin (128 SNPs) panels
  • 04Supports superpopulation and population-level predictions
  • 05Lets users train models on a custom set of AISNPs with cross-validation reports
  • 06Includes a 3D plot command and a Streamlit app for visualization

Use cases

  • Visualizing a direct-to-consumer genetic test result next to reference populations
  • Evaluating how well a custom panel of ancestry-informative SNPs separates populations
  • Teaching or demonstrating ancestry inference with 1000 Genomes data
  • Batch-predicting ancestry for a cohort of genotype files

Quick start

  1. 1

    Install ezancestry with pip

    pip install ezancestry
  2. 2

    Predict ancestry from your direct-to-consumer genetic data file

    ezancestry predict mygenome.txt
  3. 3

    Visualize the predictions in a 3D scatter plot in your browser

    ezancestry plot predictions.csv

Things to know

  • Predictions rely on only a small set of ancestry-informative SNPs compared against 1000 Genomes samples, so results are approximate.
  • Not intended for medical or clinical decisions; it is a research and exploration tool.

In collections

Data science courses & tools

Topics

#genomics#ancestry#machine-learning#bioinformatics#personal-genomics#data-visualization#streamlit#dimensionality-reduction#genomics-visualization#genotypes

FAQ

What is ezancestry?
Python tool that predicts a person's genetic ancestry from direct-to-consumer SNP data by comparing it against 1000 Genomes samples. ezancestry predicts genetic ancestry from raw direct-to-consumer genetic files such as 23andMe and ancestry.com output, as well as VCF files. It places a user's genotypes alongside more than 2,500 samples from the 1000 Genomes Project and uses a k-nearest neighbors classifier trained on ancestry-informative SNPs (AISNPs) to assign continental and regional population labels.
Is ezancestry free to use? What license does it have?
ezancestry is open source under the MIT license. Check the license terms before using it in commercial products.
Is ezancestry still maintained?
Updated within 6 months. The last commit to ezancestry was on Oct 7, 2026.
What can I use ezancestry for?
Visualizing a direct-to-consumer genetic test result next to reference populations Evaluating how well a custom panel of ancestry-informative SNPs separates populations Teaching or demonstrating ancestry inference with 1000 Genomes data Batch-predicting ancestry for a cohort of genotype files
How do I install ezancestry?
Install ezancestry with pip: pip install ezancestry Predict ancestry from your direct-to-consumer genetic data file: ezancestry predict mygenome.txt Visualize the predictions in a 3D scatter plot in your browser: ezancestry plot predictions.csv
Where can I get ezancestry?
The source code and installation instructions are on GitHub: https://github.com/arvkevi/ezancestry

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