agricola 0.4.0

Admixed GWAS for Related Individuals Conditioning On Local Ancestry

agricola

agricola is a Python package and command-line tool for conducting genome-wide association studies (GWAS) in admixed populations. Inspired by regenie and Tractor, agricola provides a scalable, local-ancestry–aware framework that handles relatedness, population structure, and ancestry effect heterogeneity.

Full documentation can be found here

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Why agricola?

Admixed individuals have unique LD patterns that can improve signal localization and improve power for population-specific causal variants. However, standard GWAS tools fail to adjust for local ancestry or model effect heterogeneity in admixed individuals.

Tools like Tractor and SAIGE-Tractor address this gap. agricola follows the same conceptual approach-performing single-variant association tests with explicit local ancestry adjustment-but combines it with:

• Accelerated linear algebra via JAX
• CUDA GPU, TPU, or CPU support for flexible compute environments
• Efficient local ancestry queries using lanctools
• Multi-phenotype modeling
• Adjustment for sample relatedness

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Installation

Requirements: Python 3.10+

Install via pip:

pip install agricola

For GPU or TPU support:

pip install agricola[cuda]

pip install agricola[tpu]