Prerequisites

FedGWAS requires Python 3.11+ and PLINK.

Python

FedGWAS requires Python 3.11+. We recommend using uv or conda to manage the Python environment and dependencies.

You can install Python from the official Python website, or using a package manager like apt on Debian-based systems, brew on macOS, or chocolatey on Windows.

PLINK

The pipeline calls PLINK for binary dataset creation, missingness checks, genotype counts, KING-based relatedness screening, and logistic-regression association screening.

Input genotypes use PLINK 1.9 binary format. KING kinship estimation uses PLINK 2 --make-king-table. VCF input is supported via conversion to PLINK-compatible representations where configured.

1. Install PLINK 1.9 so that plink is on PATH, or use the bundled project-local binaries under plink/plink_linux, plink/plink_mac, or plink/plink_win.
2. For KING-based relatedness screening, keep PLINK 2 available as plink2 in the matching bundled directory or on PATH.
3. Verify that client (center) configuration values use the PLINK prefix without .bed, .bim, or .fam extensions.

Remember to add the PLINK executables to your system's PATH variable if you choose to install them globally.

Instructions on how to modify system PATH variables:

• windows: https://www.architectryan.com/2018/03/17/add-to-the-path-on-windows-10/
• mac or linux: https://www.digitalocean.com/community/tutorials/how-to-view-and-update-the-linux-path-environment-variable

Quick Installation

FedGWAS is available on PyPI. Install it in a clean Python 3.11+ environment, and make sure plink and plink2 are discoverable on PATH:

python -m venv .venv
source .venv/bin/activate # or windows powershell .\.venv\Scripts\Activate.ps1
python -m pip install --upgrade pip
pip install FedGWAS

verify the installation:

python --version
fedgwas-sim --help