$100

Variant analysis with GATK 4 Workshop

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Sidra Medicine, Outpatient Clinic, 6th floor, room 301

Sidra Medicine

Doha

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Description

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.


Preparing for the workshop

Instruction in this link https://broad.io/gatk-w-prep and make sure you qualify prior registering as the number of seat is limited to 40 participants for this workshop.

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).



More details and program schedule, please visit events.sidra.org

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Sidra Medicine, Outpatient Clinic, 6th floor, room 301

Sidra Medicine

Doha

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