GATK Best Practice Course

The Genome Analysis Toolkit or GATK is a widely used software package developed at the Broad Institute to perform variant discovery analysis on high-throughput sequencing data.

Workshop

This workshop will cover key concepts involved in applying the GATK Best Practices for variant discovery.

There are two options for course registration:

  1. One day course: Theory and methodology of the Best Practices (Lecture series)
  2. Two day course: Theory and methodology of the Best Practices (Lecture series) and Hands-on Tutorials: Application of the Best Practices to real datasets (attendance limited to 30 participants).

Course outlines:

Day 1 – Theory and methodology of the Best Practices (Lecture series) 

  • Introduction to Variant Discovery and the GATK Best Practices workflows
  • Pre-processing tools and algorithms
  • Germline variant discovery (SNPs and Indels)
  • Somatic variant discovery (SNPs, Indels and CNVs)

Day 2 – Hands-on Tutorials: Application of the Best Practices to real datasets

  • Joint Variant Discovery: apply the GVCF workflow and interpret results.
  • Variant Callset Filtering and Evaluation: use tools to evaluate and filter a variant callset.

Scientific Co-ordinators

  • Dr Geraldine Van der Auwera (Broad Institute, USA)

Workshop Co-ordinator

  • Katherine Champ (Bioplatforms Australia, Sydney)

Workshop Dates

One-day Lecture Series

City Location Date
Sydney University of New South Wales  1st February 2016
Melbourne University of Melbourne  3rd February 2016

  Two-day Lecture Series and Hands-on Workshop

City Location Date Cost
Sydney University of New South Wales  1st-2nd February 2016 $165.00 (plus GST)
Melbourne VLSCI and University of Melbourne  3rd-4th February 2016 $165.00 (plus GST)

 

Recommended Participants

This workshop is aimed at a mixed audience of researchers who are new 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 the genomics field. Basic familiarity with the unix command-line environment is expected for the hands-on tutorials.

Draft Program

Time Subject
Day 1 –Theory and methodology of the Best Practices 
9:45 – 10:00  Registration and Welcome
10:00 – 11:00 Introduction to Variant Discovery Analysis Pre-processing Strategies
11:00 – 11:30 Break
11:30 – 11:30 Marking Duplicates Indel Realignment Base Recalibration
13:00 – 14:00 Lunch
 14:00 – 16:00 Germline Variant Calling & Joint Genotyping Filtering Variants with VQSR Genotype Refinement Workflow Callset Evaluation Break
16:00- 17:00 Somatic Variant Calling with Mutect 2 Somatic CNV Calling Closing Remarks
Day 2 – Hands-on Tutorials: Application of the Best Practices to real datasets
9:00 – 10:30 Joint Variant Discovery
10:30 – 10:45 Break
10:45-12:30 Joint Variant Discovery (Cont.)
12:30 – 13:30 Lunch
13:30-15:00 Variant Callset Filtering and Evaluation
15:00 – 15:15 Break
15:15 – 17:00 Variant Callset Filtering and Evaluation (Cont.)
17:00 – 17:30 Closing remarks & workshop surveys
 

Registration

Registrations Closed. Workshop places are limited on day 2 due to the significant practical component of this workshop. To manage high demand, all workshop applicants are subject to a selection process and must complete the online application. Successful applicants will be notified no later than the 15th of January 2016. The workshop fee covers course material, computer access, lunch and refreshments.

Contact

For further information regarding this workshop please contact Katherine Champ at kchamp@bioplatforms.com.

Training Updates

Bioplatforms Australia Training

kchamp@bioplatforms.com
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Interested in Hosting a Bioinformatics Workshop?

If you are interested in hosting a bioinformatics workshop at your local organisation or institute please contact Katherine Champ on kchamp@bioplatforms.com.
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The Genome Analysis Toolkit or GATK is a software package for analysis of high-throughput sequencing data, developed by the Data Science and Data Engineering group at the Broad Institute.

For more information please visit the Broad Institutes website: https://software.broadinstitute.org/gatk/