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Programs to perform genome-wide association studies (GWAS) are usually run via the command line. This can be intimidating for a biologist. Take me as an example: In my bachelor and master I’ve studied molecular medicine. So my formal training focused on understanding pathophysiological processes in the human body and how to perform wet-lab experiments, I never had to use the command line. Nevertheless, I recently ran my first GWAS using the nf-gwas pipeline.

Here, I want to first introduce this pipeline through the lens of a biologist and second share with you my setup. Since I am working on a Windows computer, I need to access a remote Linux server to run the pipeline. So the first section will be about the kind of tasks that are so basic that bioinformaticians don’t even talk about them. I guess this is like describing how to pipet for a trained wet-lab biologist.

However, I hope it will show you that if you follow these steps you can run your first GWAS without any prior knowledge in bioinformatics in no time :).