GWASPipe

A Python tool, based on GWASLab, for assembling a computational pipeline to standardise, QC, harmonise, convert and plot summary statistics in genetic association studies (GWAS).

Table of Contents

• Requirements
• Getting Started
• Usage
• Example Configuration Files
• Contributing

Requirements

To use GWASPipe, you'll need:

• Python 3.10 or higher
• The following dependencies installed:
  • click for command-line interface
  • cloup for file handling and metadata management
  • loguru for logging
  • ruamel-yaml for YAML parsing and generation
  • pandas for data manipulation and analysis
  • pyarrow for high-performance data processing
  • numpy for numerical computations
  • matplotlib for plotting
  • gwaslab for handling sumstats

see pyproject.toml

Getting Started

You can use one of the following ways for installing Gwaspipe.

Installation via Conda/Mamba

1. Clone the repository using Git: git clone https://github.com/your-username/gwaspipe.git
2. Create a conda environment: conda env create -n gwaspipe -f environment.yml
3. Activate it: conda activate gwaspipe
4. Install gwaspipe: make install

This will install snakemake into an isolated software environment

5. Run the tool: gwaspipe --help

Docker image

Gwaspipe is available also as a Dockerfile

1. Build the image locally: docker build -t gwaspipe:latest .
2. Run it: docker run -t -i gwaspipe:latest gwaspipe --help

The Linux OS image is available from the github packages repository: Docker image

Usage

GWASPipe provides a command-line interface (CLI) for easy usage. You can customize the behavior of the tool by providing configuration files in YAML format.

The CLI takes the following arguments:

• -c or --config: Path to the configuration file
• -i or --input: Path to the summary statistics file
• -f or --format: Format of the input file (vcf, gwaslab, regenie, fastgwa, ldsc, fuma, pickle, metal_het)
• -o or --output: Path where results should be saved
• -s or --input_file_separator: Input file separator
• -q or --quiet: Set log verbosity
• --study_label: Input study label, valid only for VCF files
• --pid: Preserve ID

Example configuration files are provided in the examples directory.

Example Configuration Files

The following example configuration files demonstrate how to customize GWASPipe:

• config_harmonize_VCF_sumstats.yml: a sample configuration file for harmonizing summary statistics in gwas-vcf format

Contributing

We welcome contributions to GWASPipe! If you'd like to contribute, please follow these guidelines:

1. Fork the repository on GitHub: https://github.com/your-username/gwaspipe.git
2. Create a new branch for your changes: git checkout -b feature/your-feature-name
3. Make your changes and commit them: git add . && git commit -m "Your commit message"
4. Push your changes to the remote repository: git push origin feature/your-feature-name
5. Open a pull request on GitHub to propose your changes

We appreciate your contributions and look forward to seeing GWASPipe grow!