postgwas-tools

postgwas-tools is a Python package that provides a collection of tools for post-GWAS (Genome-Wide Association Study) analysis, annotation, and visualization.
It simplifies steps such as plotting, SNP annotation, and result parsing for large-scale GWAS projects.

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Installation

Option 1 — From source

git clone https://github.com/neurospin/postgwas-tools.git
cd postgwas-tools
python3 -m venv venv
. venv/bin/activate
pip install -e .

Option 2 — From PyPI (planned)

pip install postgwas-tools

Option 3 - remote install from Neurospin to irene (preferred)

To install the phecovbabel pacakge as a pcocc-rs image on irene!

• install the installing tools from https://github.com/neurospin-brainomics/InstallerTGCC
• run the following commands

git clone https://github.com/neurospin/postgwas-tools.git
cd postgwas-tools
# push-docker-tgcc.sh is a command from InstallTGCC
push-docker-tgcc.sh -s `pwd` -d postgwas -t 1.0 -r n4h00001rs
# connect TGCC
pcocc-rs run n4h00001rs:postgwas-1.0 -h

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Package Structure

src/postgwas_tools/
├── annot/
│   ├── fuma/                 # FUMA-related post-GWAS visualization
│   ├── ldsc/                 # LD Score Regression utilities
│   ├── magma/                # MAGMA annotation helpers
│   ├── replication/          # Replication and cross-cohort checks
│   └── utils.py              # Common helper functions
└── mostest/                  # MOSTest-specific result processors

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Documentation & Workflows

For detailed usage examples, including QQ plots, locus-based analysis, and replication workflows, see: WORKFLOW.md

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Dependencies

• Python ≥ 3.9
• pandas, numpy, matplotlib, seaborn, scipy, qmplot, h5py

All dependencies are automatically installed when you run pip install -e ..

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Citation

If you use postgwas-tools in your work, please cite:

Dufournet A. postgwas-tools: a Python suite for streamlined post-GWAS analysis. CEA NeuroSpin, 2025.

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Links

• LICENSE
• Homepage
• Issue Tracker