Introduction

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 was able to run my first GWAS using the nf-gwas pipeline.

Here, I want to first introduce this pipeline through the lens of a biologist (see section Pipeline Overview) 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 section Mastering the basic tasks 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 :).