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  • Medicina Regenerativa
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  • Medicina Translacional

Bioinformatics for Precision Medicine: From Reads to Disease Variants - A GATK Workshop

Register by 3 April 2020 at


 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.




Day 1: 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.



09:30 - 13:00

09:30 Opening Remarks

Introduction to Sequencing Data

Introduction to Data Preprocessing

Introduction to Variant Discovery



14:00 - 16:30

Joint Calling

Introduction to Pipelining Platforms

Terra Orientation

Germline Variant Discovery Tutorial (hands-on)




Day 2: 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.



09:30 - 13:00

Variant Filtering

Genotype Refinement

Callset Evaluation

Germline Hard Filtering Tutorial (hands-on)

14:00 - 16:30

Germline CNN Tutorial (hands-on)

GWAS Case Study (hands-on)




Day 3: 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.



09:30 - 13:00

Introduction to Somatic Variant Discovery

Somatic SNVs and Indels

GATK4 Mutect2 Tutorial (hands-on)


14:00 - 16:30

Somatic CNAs

GATK4 Somatic CNA Tutorial (hands-on)

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




Day 4: 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.



09:30 - 13:00

WDL and Cromwell Basics

Hello World WDL Tutorial (hands-on)

WDL puzzles


14:00 - 16:30






Day 5: 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.



09:30 - 13:00

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

13:30 Wrapup