Course outline

The workshop focuses on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. Participants will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of their dataset. In the course of this workshop, we highlight key functionalities such as the GVCF workflow for joint discovery of germline short variants in cohorts, somatic short variant discovery using Mutect2, and copy number variation discovery using GATK-CNV. We also exercise the use of pipelining tools to assemble and execute GATK workflows.

Hands-on sessions

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 FireCloud, our publicly available, secure cloud-based analysis service.

Computing facilities for running the exercises in the hands-on session, will be provided by DTU Computerome, but participants should bring their own laptop in order to access the remote computer. More detail will be provided later.

Target audience

This workshop is aimed at a mixed audience of people who are new to the topic of variant discovery or to GATK, seeking an introductory course into the tools, or who are already GATK users seeking to improve their understanding of and proficiency with the tools. Participants should already be familiar with the basic terms and concepts of genetics and genomics. Basic familiarity with the command line environment is required.


Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points.

Number of participants

There are only ~30 seats available for the hands-on sessions. Ph.D. students will be prioritized for this part of the course, but lectures are open for all.


Rasmus Froberg Brøndum, Andreas Petri


External lecturers from the Broad Institute

ECTS: 2.8

Januar 29 - February 1, 2019

Deadline: December 21, 2018

Auditorium, ACM15, AAU CPH, A.C. Meyers Vænge 15

City: Copenhagen