Pre-requisites

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, and logistic regression.

1. Use the bundled project-local binaries under plink/plink_linux, plink/plink_mac, or plink/plink_win, or install PLINK on PATH.
2. For KING, keep PLINK 2 available as plink2 in the matching bundled directory or on PATH.
3. Verify that center configuration values use the PLINK prefix without .bed, .bim, or .fam extensions.

You can also download PLINK from the official website: https://www.cog-genomics.org/plink/2.0/. Follow the installation instructions for your operating system, and ensure that the PLINK executable is accessible from your command line. Remember to add PLINK to your system's PATH variable if you choose to install it 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