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Variant analysis with GATK

Date: 13.09.2017 9:00 - 15.09.2017 17:00
Location details: The lecture day (13.9) is organised in Biomedicum Helsinki, while the hands-on days (14.-15.9) take place in the computer classroom Dogmi located in the premises of CSC at Keilaranta 14, Espoo.
Language: English
Lecturers: Geraldine Van der Auwera (MIT Broad)
Kate Voss (MIT Broad)
Megan Shand (MIT Broad)
Price: The registration fee is 60 euros + VAT per day. The fee covers morning and afternoon coffees. DPBM students register for free using their separate DPBM registration form, which will open in August.
Registration by 13.08.2017 23:00
The seats are filled in the registration order. If a cancellation is received five (5) business days prior to the course, the course fee will be refunded with the exception of a handling fee of 10 €. For no-shows and cancellations after that no refunds will be made. Registration can be transferred to someone else from the same organization without additional charge.

Payment can be made with electronic invoicing, credit card, or direct bank transfer. Note that for electronic invoicing you need the operator and e-invoicing address (OVT code) of your organization. Please also note that invoice reference is needed for electronic invoicing in your organization, so please have this available when registering.
Additional information

This workshop will focus on the core steps involved in calling variants with the Broad Institute's Genome Analysis Toolkit (GATK), 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. This course is organized in collaboration with the Doctoral Programme in Biomedicine (DPBM) of University of Helsinki.

This workshop highlights key functionalities such as the germline GVCF workflow for joint variant discovery in cohorts, RNAseq­ specific processing, and new somatic variant discovery capabilities in GATK4. It also demonstrates the use of pipelining tools to assemble and execute GATK workflows.

Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non­human 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.

Program outline

The workshop is composed of one day of lectures and two optional days of hands-on training, structured as follows:

Day 1: lectures: Rationale, theory and application of the GATK Best Practices for Variant Discovery in high-throughput sequencing data.

Day 2 AM: hands-on: Germline variant discovery (SNPs, Indels)
Day 2 PM: hands-on: Germline variant filtering (SNPs, Indels)

Day 3 AM: hands-on: Somatic variant discovery (SNPs, Indels, CNV)
Day 3 PM: hands-on: Pipelining on the cloud with Workflow Description Language, WDL

In the optional hands-on sessions focused on analysis, we walk attendees 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 Samtools, IGV, RStudio and RTG Tools.
In the optional hands-on session on pipelining, we walk attendees through exercises that teach them to write workflow scripts using WDL, the Broad's new Workflow Description Language, and to execute these workflows locally as well as through publicly available cloud-based services.

Detailed agenda of the Best Practices lectures 13.9.2017

Introduction to variant discovery analysis and GATK Best Practices
Coffee Break
Marking Duplicates
Base Recalibration
Lunch Break
Variant Calling and Joint Genotyping
Filtering variants with VQSR
Genotype Refinement Workflow
Coffee Break
Callset Evaluation
Somatic SNV and indel discovery with MuTect2 in GATK4
Somatic CNV discovery with GATK4

Target audience and prerequisites

The lecture day of 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. Attendees should already be familiar with the basic terms and concepts of genetics and genomics.

The hands-on days are aimed at novice to intermediate users who are seeking detailed guidance with GATK and related tools. Basic familiarity with the command line environment is required.

Learning objectives

After this course you should be able to:

  • Understand the overall variant discovery workflow rationale and requirements
  • Understand key methods and functionalities in light of the latest research
  • Understand key differences between germline and somatic variant discovery approaches
  • Apply analysis tools and Best Practices workflows to a real data set
  • Interpret analysis results and troubleshoot common problems
  • Write and execute WDL analysis pipelines

During this course you will learn about:

  • Pre-processing of high-throughput DNA and RNAseq sequencing data
  • Variant discovery (germline and somatic short variants, somatic CNV)
  • Germline variant filtering and evaluation
  • Pipelining strategies 


Projects and Collaboration Networks
Service Break
Projects and Collaboration Networks
Service Break