Variant calling using GATK4 command line workflow

April 28, 2022 - 10am
via zoom


Variant calling using GATK4 command line workflow

Workshop date/time (Melbourne time): Thursday 28th April 10-2pm

EOI deadline: 5pm Thursday 14th April

Successful applicants notified: Thursday 21st April

Workshop outline

This workshop aims to introduce participants to variant calling using command line applications. The material follows the GATK variant calling best practices workflow and provides an introduction to tools, datatypes and file formats associated with variant calling. The workshop will use a test llumina sequencing dataset to progress through the workflow from aligning sequencing reads to a reference genome before applying the GATK best practices workflow to call genetic variants (SNVs and Indels) in test data.

Tools used

  • BWA
  • Samtools
  • GATK4
  • picard
  • bcftools
  • jigv

During this training participants will 

  • Align reads to a reference genome
  • Call simple variants using the GATK best practices workflow
  • Be introduced to SAM/BAM and VCF file formats
  • Follow instruction to run command line applications

Lead trainer

Khalid Mahmood (Melbourne Bioinformatics, The University of Melbourne)

Who the workshop is for

Researchers with some knowledge of variant calling with some command line experience.

Due to the limited number of places available at this workshop, places will be allocated based on this expression of interest application. Please complete the registration questions and submit them before the deadline.

How to apply

The workshop is free but due to anticipated high demand, participation is subject to selection through an expression of interest process.

Deadline – 5pm Thursday 14th April

Submissions will be reviewed by our training team and all applicants advised of the status of their application (successful, waiting list, unsuccessful) by Thursday 21st April

For further information, email