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Variant Discovery with GATK4



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 germline GVCF workflow for joint variant discovery in cohorts, somatic variant discovery using MuTect2, and copy number variation discovery using GATK-CNV. All analyses are demonstrated using GATK version 4. Finally, we demonstrate the use of pipelining tools to assemble and execute GATK workflows.

The workshop covers basic genomics, all currently supported Best Practices pipelines as well as pipelining with WDL/Cromwell/FireCloud. This includes the logic of the major pipelines, file formats and data transformations involved, and hands-on operation of the tools using goal-oriented exercises.

  • Day 1: Introduction to Genomics, GATK Best Practices and Pipelining
  • Day 2: Germline short variant discovery (SNPs + Indels)
  • Day 3: Somatic variant discovery (SNVs + Indels + CNVs)
  • Day 4: Writing pipelines with WDL and running them in FireCloud

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.



  • The course is aimed primarily at mid-career scientists – especially those whose formal education likely included statistics, but who have not perhaps put this into practice since.
  • Familiarity with the basic terms and concepts of genetics and genomics.
  • Basic familiarity with the command line environment is required.
  • Sufficient UNIX experience might be obtained from one of the many UNIX tutorials available online.


For additional information, follow this link.


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