Variant calling using GATK4 command line workflow

28 June 2023 - 10am-2pm
21 Bedford St, North Melbourne, VIC 3051


Variant calling using GATK4 command line workflow

Workshop Description:

This workshop aims to introduce participants to variant calling using command line applications. The teaching material is available here and 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)

Target audience:

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


This free workshop is available to staff and students at The University of Melbourne and its affiliated institutes only (refer to ‘Members’ section).


Basic knowledge/experience of the command line is necessary for this workshop. You will need to be able to “ssh” into a remote machine, navigate the directory structure and “scp” files from a remote computer to your local computer.

If you wish to attend a refresher course we recommend you attend our “Command line skills in UNIX” workshop on May 18th, or enroll in one of the “Introduction to Linux and HPC workshop” delivered regularly by Research Computing Services.

This is a hands-on workshop and attendees must supply their own laptop with access to the internet/wifi and the following software preinstalled to log onto the cloud computer:

  • Windows users: A terminal emulator such as PuTTY (free and open-source) will need to be downloaded.
  • Software for file transfers between a local computer and remote server such as WinSCP or FileZilla.
  • Mac users: No additional software needs to be installed for this workshop.

Cloud computer

This workshop is designed for participants with command-line knowledge. It will be run on a Nectar Instance. You will be given an individual IP address and password to log on to using the SSH client tool on your computer (Terminal on Mac or PuTTY on Windows).

If you require any further information, please contact Melbourne Bioinformatics at:

LAST RUN: October 19, 2022