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.
This workshop will cover key concepts involved in applying the GATK Best Practices for variant discovery.
There are two options for course registration:
- One day course: Theory and methodology of the Best Practices (Lecture series)
- 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).
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.
- Dr Geraldine Van der Auwera (Broad Institute, USA)
- Bioplatforms Australia, Sydney
One-day Lecture Series
|Sydney||University of New South Wales||1st February 2016|
|Melbourne||University of Melbourne||3rd February 2016|
Two-day Lecture Series and Hands-on Workshop
|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)|
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.
|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|