====== 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 sessions 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 IGV and RStudio.

In the optional hands-on sessions on pipelining, we walk participants through exercises that teach them to write workflow scripts using WDL, the Broad's new Workflow Description Language, and to execute these workflows locally with Cromwell as well as through Terra, our publicly available, secure cloud-based analysis service.