GWAS Downstream Analysis Toolkit 🧬

A reproducible pipeline for post-GWAS analysis, transforming raw summary statistics into biological insights.

⭐ Features

• LD Clumping: Identifies independent lead SNPs using PLINK.
• Visualization: Generates Manhattan and Q-Q plots using the qqman R package.
• Inflation Testing: Calculates genomic inflation ($\lambda$) to check for population stratification.
• Locus Zooming: (Optional) Scripts for localized Manhattan plots around lead variants.

🛠️ Requirements

• PLINK v1.9
• R (v4.0+)
• R Libraries: qqman, data.table, ggplot2

🚀 Execution Workflow

1. Prepare Data: Download summary statistics from the GWAS Catalog.
2. Run Clumping:

   bash scripts/01_qc_clumping.sh
   
   

The pipeline outputs:

gwas_clumped.clumped: A table of independent significant loci.

manhattan_plot.png: Global visualization of associations.

qq_plot.png: Quality control plot for p-value distribution.