The Biomedical Informatics Division at Sidra Medicine is pleased to host the popular Genome Analysis ToolKit GATK workshop that will take place 6th-9th May 2018.

The workshop will be facilitated by a team from the Broad institute of MIT and Harvard led by Dr. Geraldine Van der Auwera, Associate Director of Outreach and Communications

 

Course outline

The workshop focuses on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. Participants 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 their dataset. In the course of this workshop, we highlight key functionalities such as the GVCF workflow for joint discovery of germline short variants in cohorts, somatic short variant discovery using Mutect2, and copy number variation discovery using GATK-CNV. We also exercise the use of pipelining tools to assemble and execute GATK workflows.

 

Hands-on sessions

In the hands-on sessions focused on analysis, we walk participants 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 IGV and RStudio.

In the optional hands-on sessions on pipelining, we walk participants through exercises that teach them to write workflow scripts using WDL, the Broad’s new Workflow Description Language, and to execute these workflows locally with Cromwell as well as through FireCloud, our publicly available, secure cloud-based analysis service.

 

Target audience

This 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. Participants should already be familiar with the basic terms and concepts of genetics and genomics. Basic familiarity with the command line environment is required.

Participants will be expected to bring their own laptops with software preinstalled (detailed instructions here).

 

 

Program Schedule

 

Day 1: Introduction to Genomic Analysis

Morning (9am – 12pm)

  • 09:00 Opening remarks
  • 09:15 Introduction to Sequence data / pre-processing workflow
  • 09:45 Introduction to Germline variant discovery Best Practices workflows
  • 10:15 Coffee/tea break
  • 10:45 Introduction to Somatic variant discovery Best Practices workflows
  • 11:15 Introduction to pipelining with WDL + Cromwell + FireCloud
  • 11:45 Closing question time

Lunch Time (12pm – 1pm)

Afternoon (1pm – 4pm)

  • 13:00 Mapping
  • 13:25 Marking Duplicates
  • 13:50 Base recalibration (BQSR)
  • 14:15 Coffee/tea break
  • 14:45 Hands-on data exploration

Day 2: Germline short variant discovery

Morning (9am – 12pm)

  • 9:00 Recap of germline variant discovery Best Practices
  • 9:15 HaplotypeCaller
  • 9:45 Joint-calling with GenomicsDB + GenotypeGVCFs
  • 10:15 Coffee/tea break
  • 10:45 Hands-on joint-calling

Lunch Time (12pm – 1pm)

Afternoon (1pm – 4pm)

  • 13:00 Filtering with VQSR
  • 13:30 Genotype Refinement
  • 14:00 Callset Evaluation
  • 14:15 Coffee/tea break
  • 14:45 Hands-on filtering approaches

Day 3: Somatic variant discovery

Morning (9am – 12pm)

  • 9:00 Recap of somatic variant discovery Best Practices
  • 9:15 Somatic SNVs and indels with Mutect2
  • 10:00 Coffee/tea break
  • 10:30 Hands-on Mutect2

Lunch Time (12pm – 1pm)

Afternoon (1pm – 4pm)

  • 13:00 Somatic CNVs with GATK CNV
  • 13:30 Hands-on GATK CNV
  • 14:45 Coffee/tea break
  • 15:15 Preview of upcoming methods: germline CNV and SV
  • 15:45 Open question time

 

Day 4: Pipelining

Morning (9am – 12pm)

  • 9:00 Recap of WDL/Cromwell basics
  • 9:15 Hands-on WDL/Cromwell basics
  • 10:15 Coffee/tea break
  • 10:45 Self-paced WDL exercises

Lunch Time (12pm – 1pm)

Afternoon (1pm – 4pm)

  • 13:00 Recap of FireCloud basics
  • 13:15 Hands-on FireCloud Part 1
  • 14:15 Coffee/tea break
  • 14:45 Hands-on FireCloud Part 2

 

 



Main Speakers



Programme Schedule



Starts / Ends

On       May 6, 2018
Until       May 9, 2018

9:16 am – 9:16 am


100

Variant analysis with GATK 4 Workshop



Venue Location

Sidra Medicine
Outpatient Clinic
6th floor
Room 301


Sponsors


Exhibitors