Running the pipeline

• The notebooks in Step 1: Data Extraction should be downloaded and run locally from a session logged into DNANexus, in accordance with instructions given here: https://github.com/TYTYBU/vcfByGene – All other notebooks should be uploaded to a UK Biobank/DNANexus project and run in the order given in the folders. Between each run, either refresh the directory or finish the current JupyterLab session and start a new one. Within each folder, notebooks can be run in any order.