Bioinformatics for precision medicine: From reads to disease variants

A GATK Workshop

Institut Català d'Oncologia, Barcelona, Spain

About The Workshop

About The Workshop

Massive sequencing is becoming mainstream in many fields of biomedicine, including the clinical practice.

However, the transformation of sequencing raw data into valuable biological information on variants and their further interpretation is still a complex task that requires 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 GATK Workshop is followed by a last day lecture covering topics on germline and somatic disease variant prioritization

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.


Trueta room
Catalan Institute of Oncology
Avinguda de la Granvia, 199-203
L'Hospitalet de Llobregat, Barcelona



Workshop Speakers

Speakers for the GATK Workshop

Speaker 4

Eric Banks

Senior Director of the Data Sciences Platform
Broad Institute

Speaker 3

Sushma Chaluvadi

Bioinformatics Support Specialist
Broad Institute

Speaker 2

James Emery

Software Engineer
Broad Institute

Speaker 1

Azmina Karukappadath

Software Engineer
Broad Institute

Speakers for the Variant Prioritization Tutorial

Speaker 6

Rosario Carmona

Clinical Bioinformatics Area
Fundación Progreso y Salud

Speaker 7

Javier Pérez Florido

Clinical Bioinformatics Area
Fundación Progreso y Salud

Speaker 5

Xavier Solé

Head of Unit of Bioinformatics for Precision Oncology
Catalan Institute of Oncology

Workshop Schedule (tentative)

The GATK Workshop will comprise the first 4 days of the course (Mon-Thu). On Friday there will be a tutorial on germline and cancer somatic variant prioritization.

Each day will have breaks at approximately the following times:
Morning Break 11:00am - 11:30am.
Lunch 01:00pm - 02:00pm.
Afternoon Break 3:00pm - 3:30pm.
The workshop will start on Monday at 09:30am and will end on Friday at 01:30pm.

Morning schedule will be approximately 09:30am - 01:00pm.
Afternoon schedule will be approximately 02:00pm - 04:30pm.

The first day of the workshop gives a high-level overview of various topics in the morning, and in the afternoon we show how these concepts apply to a case study. The case study is tailored based on the audience, as represented by their answers in our pre-workshop survey.

Opening Remarks (09:30am).

Introduction to Sequencing Data.

Introduction to Data Preprocessing.

Introduction to Variant Discovery.


Joint Calling.

Introduction to Pipelining Platforms.

Terra Orientation.

Germline Variant Discovery Tutorial (hands-on).

Today we dive deep into the tools that make up the GATK Best Practices Pipeline. In the morning we discuss variant discovery, and in the afternoon we look at refinement and filtering. You will have the opportunity both in the morning and in the afternoon to get hands-on with these tools and run them yourself.

Variant Filtering.

Genotype Refinement.

Callset Evaluation.

Germline Hard Filtering Tutorial (hands-on).

Germline CNN Tutorial (hands-on).

GWAS Case Study (hands-on).

Today we will cover Somatic Variant Discovery in more depth. In the morning we primarily focus on calling short variants with Mutect2, and in the afternoon we look at copy number alterations. Both sections have a paired hands-on activity.

Introduction to Somatic Variant Discovery.

Somatic SNVs and Indels.

GATK4 Mutect2 Tutorial (hands-on).

Somatic CNAs.

GATK4 Somatic CNA Tutorial (hands-on).

GATK Best Practices for SNP/Indel Variant Calling in Mitochondria (demo).

Over the last three days, you’ve learned a lot about different pipelines and tools that you can use in GATK. Today we will be learning all about how those pipelines are written in a language called WDL. In the afternoon we cover other useful topics to working on the cloud, including Docker and BigQuery.

WDL and Cromwell Basics.

Hello World WDL Tutorial (hands-on).

WDL puzzles.



The last day of the course will cover topics related to the bioinformatics analysis and prioritization of cancer somatic alterations using gene panels, and also the prioritization of germline variants. This part of the course will be instructed by specialists from the Catalan Institute of Oncology and the Fundación Progreso y Salud.

Clinical cancer somatic profiling with DNA and RNA cancer gene panels.

Introduction to bioinformatics analysis of Illumina TSO500.

Tools for annotation and prioritization of cancer somatic variants (hands-on).


Introduction to openCGA and MMP for variant prioritization.

Self-paced germline variant prioritization with MMP.

Wrapup (01:30pm).

Workshop Venue

Workshop venue information

Catalan Institute of Oncology

Hospitalet de Llobregat, Barcelona, Spain

Room: Aula Trueta (1st floor).

How to get there.


The Catalan Institute of Oncology is located in the Hospital Duran i Reynals building in L'Hospitalet de Llobregat (a city just next to Barcelona). You can reach the building by public transportation (bus, metro). Once you enter the building through the main entrance you will see signs that will guide you to the Trueta room, where the course will take place.

Social dinner Venue

Social dinner venue information

Coming soon


Coming soon


The Spanish National Bioinformatics Institute (INB) is the ISCIII Bioinformatics platform. Its Coordination Node is supported by grant PT17/0009/0001, of the Acción Estratégica en Salud 2013-2016 of the Programa Estatal de Investigación Orientada a los Retos de la Sociedad, funded by the Instituto de Salud Carlos III (ISCIII) and European Regional Development Fund (ERDF).

Frequently Asked Questions

Register (Coming soon)

Standard registration
250 EUR

  • Full access to the 5-day workshop
  • Morning and afternoon coffee breaks
  • Lunch
  • Social dinner

Full registration
295 EUR

  • Full access to the 5-day workshop
  • Morning and afternoon coffee breaks
  • Lunch
  • Social dinner

Contact Us

For more information you can reach us at the following contact details:


Olga López
Oncology Data Analytics Program
Catalan Institute of Oncology
Av. de la Granvia de L'Hospitalet 199-203
08908 L'Hospitalet de Llobregat, Barcelona

Phone Number

+34 93 260 71 86