GATK Workshop 2023

13 - 17 Nov Granada, Spain
From reads to diagnostic and secondary findings
5-day workshop

About this workshop

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.

This 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 tertiary analysis (diagnostic and secondary findings) using the tools developed by the Platform of Computational Medicine. 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.

Pre-registration closes in:


Andalusian Platform for Computational Medicine, Fundación Progreso y Salud, Departamento de Ingeniería de Computadores, Automática y Robótica, Universidad de Granada, CIBERER, Broad Institute
andalusian platform medicine
fundacion progreso y salud
broad institute


Broad Institute of MIT and Harvard - GATK team (GATK workshop)
Lee Lichtenstein
Computational Methods at Broad Institute of MIT and Harvard
George Grant
Principal Software Engineer
Data Science Platform
Andrey Smirnov
Machine Learning Engineer
Cambridge, Massachusetts

Andalusian Platform for Computational Medicine (tutorial on tertiary analysis)
Javier Pérez Florido
Postdoctoral Researcher
Fundación Progreso y Salud
Rosario Carmona Muñoz
Postdoctoral Researcher
Fundación Progreso y Salud
José Luis Fernandez Rueda
Engineer of the Andalusian Platform for Computational Medicine
Fundación Progreso y Salud

Target audience

The 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 (detailed instructions will be posted two weeks before the course) unless the workshop host provides a computer lab.

Attendance is typically limited to 30 or 40 participants depending on the number of trainers and the size of the room that is available.

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.

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.


Day 1 - Introductions and Germline Variant Discovery

09:15 - 13:30


What is this workshop going to teach you over the next few days? We outline the schedule and order of topics before beginning detailed instruction.

  • Registration and Welcome
  • Opening Remarks
  • Introduction to GATK
  • Introduction to sequencing data
  • Introduction to pre-processing
  • Coffee break
  • Introduction to pipelining
  • Getting Started with Pipelining

13:30 - 14:30

Lunch Break

14:30 - 17:00


  • Germline Variant Discovery, incl. HaplotypeCaller
  • Germline Variant Discovery (hands-on)
  • Coffee Break
  • Joint Calling
  • General Q&A

Day 2 - Variant Filtering & Evaluation and Long Reads

09:30 - 13:30


We will continue learning about analyzing germline variants and finish with some overviews of newer technologies: long reads and DRAGEN-GATK

  • Using Large Cohorts
  • Case Study: Germline Variants (hands-on)
  • Introduction to Variant Filtering
  • Coffee break
  • Genotype Refinement
  • Callset Evaluation

13:30 - 14:30

Lunch Break

14:30 - 17:00


  • VQSR (hands-on)
  • Coffee break
  • Intro to DRAGEN-GATK
  • Processing Long Reads
  • General Q&A

Day 3 - Somatic Variants and CNVs

10:00 - 13:30


We will learn about somatic SNP/Indel and both germline and somatic copy number variants (CNVs)

  • Running refinement and evaluation tools (hands-on)
  • Intro to Somatic Variant Discovery
  • Somatic SNVs and Indels
  • Coffee break
  • Messing around with Mutect2 (hands-on)
  • Intro to Somatic CNVs

13:30 - 14:30

Lunch Break

14:30 - 17:00


  • Somatic CNVs (hands-on)
  • Coffee break
  • Germline Copy Number Variation
  • General Q&A

Day 4 - Mitochondria, Germline CNVs, and scRNA-seq

10:00 - 13:30


We will learn about genomic sequencing methods for additional data types.

  • Guided Demonstration of Mitochondria Data
  • Introduction to calling Structural Variants with GATK-SV
  • Coffee break
  • gCNV pipeline (hands-on)

13:30 - 14:30

Lunch Break

14:30 - 17:00


  • Introduction to single-cell RNA-seq analysis
  • Coffee break
  • Single-cell RNA-seq analysis (hands-on)
  • Workshop wrap-up and survey
  • General Q&A


Networking dinner

To be defined

Day 5 - Analysis of diagnostic and secondary findings

10:00 - 13:30


Over the last four days, you've learned about different pipelines and tools that you can use in GATK for variant discovery, obtaining a huge set of genomic variants (millions in the case of whole genome sequencing) that have to be handled. From this set of variants, diagnostic variants (those that answer or partly answer the clincial question) have to be identified. Optionally, secondary findings (variants relevant to health perspectives and/or reproductive decisions) are also important. Today, we will be learning the bionformatic tools developed by the Platform of Computational Medicine for the analysis of diagnostic and secondary findings.

  • Basics on diagnostic and secondary findings. Tools
  • Coffee Break
  • Self-paced variant prioritization for diagnostic and secondary findings
  • Wrap-up and course closing

Course application


Registration includes access to the course, coffee break (monday to friday) and lunch (monday to thrusday)


Venue and social events

  • CMAT (Complejo Multifuncional Avanzado de Simulación e Innovación Tecnológica). Averroes room
  • Health Sciences Technology Park (Parque Tecnológico de la Salud)
  • 21, Avenida de la Investigación, 18016 Granada
  • Location

How To Get Here

Facilities & Accommodations

Hotels with a close tramway stop

Hotel Occidental Granada ****

  • Calle Alhamar, 46s 18004 Granada (Tramway stop: Recogidas)
  • Tel: (+34) 958 290 303
  • 10 minutes by car to CMAT.

Hotel Andalucía Center ****

  • Avenida Fuente Nueva, s/n 18002 Granada (Tramway stop: Hípica)
  • Tel: (+34) 958 181 500
  • 8 minutes by car to CMAT.

Hotel Abades Nevada Palace ****

  • C/ de la Sultana, 3 - Granada (Tramway stop: Palacio Deportes)
  • Tel: (+34) 902 222 570
  • 4 minutes by car to CMAT

Other hotels

Hotel Urban Dream Nevada ***

  • Calle Benjamín Franklin, 3
  • 18100 Armilla (Granada)
  • Tel: (+34) 958 985 020
  • 7 minutes by car to CMAT

Hotel Ibis Granada *

  • HOTEL CIUDAD 1* 18100
  • Armilla (Granada)
  • Tel: (+34) 958 184 250
  • 9 minutes by car to CMAT