Takeaway: Tractor Nextflow makes ancestry-aware GWAS harmonized, reproducible, and scalable, helping researchers include admixed individuals and uncover genetic signals missed by traditional methods.

We also provide pre-curated LAI reference panels for 2-way AFR–EUR and 3-way AFR–EUR–AMR from TGP-HGDP reference dataset.

Check: github.com/Atkinson-Lab...

Tractor Nextflow Workflow solves this:
* Automates all steps from QC’d VCF to Tractor GWAS
* Modular & scalable
* Supports multiple tools: SHAPEIT5, RFMix2, FLARE, GNomix
* Can run anywhere: local, HPC, cloud

However, running Tractor is a multi-step process:
* Module 1: Accurate phasing
* Module 2: Local ancestry inference
* Module 3: Tractor GWAS

This means multiple tools, scripts and reference panels to decide from.

Solution: Tractor GWAS
* Models local ancestry for robust association testing
* Produces ancestry-specific summary statistics
* Detects ancestry-enriched hits missed by standard GWAS

Documentation: atkinson-lab.github.io/TractorWorkf...

Problem: Admixed individuals are often excluded due to population stratification, even though they make up a substantial portion of modern biobanks. This could lead to missed genetic discoveries.