IKMB Association Testing Pipeline for mGWAS and PheWAS

1. What happens in this pipeline?
2. Installation and configuration
3. Running the pipeline
4. Output
5. Troubleshooting

This repository builds on and extends scripts previously released by our group in the BIGwas/gwas-assoc framework. The original software was published in:

Kässens JC, Wienbrandt L, Ellinghaus D. BIGwas: Single-command quality control and association testing for multi-cohort and biobank-scale GWAS/PheWAS data. Gigascience. 2021 Jun 29;10(6):giab047. DOI: 10.1093/gigascience/giab047

If you use this repository in published work, please cite the BIGwas methods paper above. Please also retain the original copyright and license notices, in accordance with the MIT License.