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Variant analysis with GATK



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 GVCF workflow for joint variant discovery in cohorts, RNAseq ­specific processing, and somatic variant discovery using MuTect2. We also preview capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery.

The workshop is composed of one day of lectures (including many opportunities for Q&A) and one day of hands­on training. On the first day, we explain the rationale, theory and application of our Best Practices for Variant Discovery in high­-throughput sequencing data. On the second day, we walk attendees through hands­on exercises that teach how to manipulate the standard data formats involved in variant discovery and how to apply GATK tools appropriately to various use cases and data types. In the course of these exercises, we demonstrate useful tips and tricks for interacting with GATK, dealing with problems, and using third­party tools such as Samtools, IGV and RStudio.

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.



Geraldine Van der Auwera, Broad Institute


Audience and Prerequisites

  • The lecture­based component 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.

  • The hands­on component is 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.

  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals.


Syllabus, Tools and Resources

During this course you will learn about:

  • Variant detection for next-generation DNA sequencing
  • Data pre-processing
  • Variant discovery
  • Variant functional annotation and evaluation


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
  • Apply the Best Practices tools and workflow to a real data set
  • Interpret analysis results and troubleshoot common problems



Book Here

GATK website



Day 1 Lectures 
Introduction to variant discovery analysis and GATK Best Practices 
Coffee Break 
Marking Duplicates Indel Realignment Base Recalibration 
Lunch Break 
Variant Calling and Joint Genotyping Filtering variants with VQSR Genotype Refinement Workflow 
Coffee Break 
Callset Evaluation
Somatic variant discovery with MuTect2 Preview of CNV discovery with GATK4 
Day 2 Hands­on exercises 
Working with standard data formats and data types: BAM, VCF, WGS, WEx, RNAseq Running Picard and GATK tools to process sequence data and collect QC metrics 
Coffee break 
Variant calling with HaplotypeCaller and the GVCF workflow 
Lunch break 
Variant callset evaluation and filtering 1 
Coffee break 
Variant callset evaluation and filtering 2 


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