From reads to disease variants: GATK Workshop and Disease variant prioritization tutorial - Granada, Spain

Event start date
21-10-2019 09:15
Event end date
25-10-2019 13:30
GATK Workshop. Granada, 2019


The Clinical Bioinformatics Area at Hospital Virgen del Rocío from Seville is pleased to host the popular Genome Analysis ToolKit GATK workshop that will take place in Granada on 21th - 25th October 2019.

  • GATK Workshop - October 21-24, 2019
  • Disease variant prioritization tutorial - October 25, 2019


Massive sequencing is becoming mainstream in many fields of biomedicine, including the clinical practice. However, the management of sequencing raw data to transform them into valuable biological information on variants and its further interpretation is still a complex task that requires of intensive computing and trained personnel.

The 5-day "From reads to disease variants" course covers all the steps from the raw sequencing data, produced by the sequencers, to the obtention of lists of variants using the popular GATK software. The course is followed by a tutorial on the IVA, a powerful and intuitive web interface for the interactive prioritization and detection of disease variants. GATK workshops are designed to provide a comprehensive onboarding experience to new users, as well as access to more advanced understanding for users who are already familiar with the toolkit.



This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You 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 your dataset. In the course of this workshop, we highlight key functionalities such as the germline GVCF workflow for joint variant discovery in cohorts, somatic variant discovery using MuTect2, and copy number variation discovery using GATK-CNV. All analyses are demonstrated using GATK version 4. Finally, we demonstrate the use of pipelining tools to assemble and execute GATK workflows. The workshop covers basic genomics, all currently supported Best Practices pipelines as well as pipelining with WDL/Cromwell/FireCloud.

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.

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. Participants will be expected to bring their own laptops with software preinstalled.

See more information like program schedule and registration instructions at GATK2019 Workshop Wiki