Welcome to the KnockOffGWAS pipeline webpage!

The main purpose of this website is to provide a practical step-by-step guide to performing KnockOff GWAS on a genetic dataset. This will take the form of following a real data analysis using the pipeline. Crucially, the pipeline includes everything that is necessary to perform the analysis starting with your genetic data. This takes the form of generic scripts that can be used with any data which includes all intermediate steps to create and convert data where necessary.

Please use the menu to the left to navigate through the documentation.

Citation

Please use the following conference abstract [1] to reference the pipeline before a better reference is available:

@inproceedings{howey:etal:26,
author    = {Howey, R AND Cordell, H J},
title     = {A Practical End-to-End Pipeline for KnockoffGWAS with Application to Primary Biliary Cholangitis GWAS Data},
booktitle = {EMGM 2026},
year      = {2026},
address   = {Davos, Switzerland}
}

Contents

• Introduction
• Download
• Overview
• Step 1. File Preparation
  • Initial data preparation
  • Quality control of data
  • Setup directories for analysis
  • Create script “set_dirs.sh” to point to dataset directory
  • Running data preprocessing
• Step 2. Performing KnockOffGWAS
  • Removing temporary files
• Step 3. BOLT-LMM Analysis
• Step 4. Visualisation
• Conclusions
• Pipeline Container
  • Setup
  • Data preprocessing
  • Analysis
  • BOLT-LMM Analysis
  • Removing temporary files
  • Visualisation
• References

Contact

Please contact Richard Howey with any queries.