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 daycourse: 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.
CallsetFiltering and Evaluation: use tools to evaluate and filter a variant callset.
- Dr Geraldine Van der Auwera (Broad Institute, USA)
- Katherine Champ (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
|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
|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
|16:00- 17:00||Somatic Variant Calling with
|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|
|15:00 – 15:15||Break|
|15:15 – 17:00||Variant
|17:00 – 17:30||Closing remarks & workshop surveys|
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.
For further information regarding this workshop please contact Katherine Champ at firstname.lastname@example.org.
Bioplatforms Australia Trainingkchamp@bioplatforms.com
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 email@example.com.
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/