Goals of the hands-on exercises

The hands-on exercises are designed to teach participants concrete skills and enable them to use the tools in their own research. In the hands-on exercises focused on analysis, we walk participants through exercises that teach them how to manipulate the standard data formats involved in variant discovery and how to apply GATK tools appropriately to common use cases and data types. In the course of these exercises, we demonstrate useful tips and tricks for interacting with GATK and Picard tools, dealing with problems, and using third-party tools such as Samtools, IGV and RStudio. In the hands-on exercises focused on pipelining, we walk participants through exercises that teach them to write workflow scripts using WDL (Workflow Description Language), and to execute these workflows locally as well as through FireCloud, our publicly available secure cloud-based analysis service. Access to the service is free, and free credits are provided to cover the cost of compute and storage on Google Cloud. Participants will perform the exercises on their own laptops. By the end of the workshop, participants can expect to know how to use key file formats, compose GATK command-lines for all major analysis steps, identify and interpret outputs, as well as compose and execute GATK pipelines.