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.
Documentation
Full documentation, including examples, methods description, and details can be found here: https://frankp-0.github.io/agricola
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:
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