Variant calling using GATK4 command line workflow – applications close 10 September

Khalid Mahmood, Melbourne Bioinformatics, The University of Melbourne

Who is the workshop for?

Researchers and students at The University of Melbourne and its affiliated institutes only (refer to ‘Members’ section) with some knowledge of variant calling with some command line experience.

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, Monday 10 September 2021 Submissions will be reviewed by our training team and all applicants advised of the status of their application (successful, waiting list, unsuccessful) by Thursday 13 September 2021.

Requirements

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. This is a hands-on workshop held in a zoom meeting room and using command line tools installed on a cloud computer. Attendees must use 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 Zoom meeting room and command line tools installed on a cloud computer. This workshop 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).

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 data 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.

Learning Objectives

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 instructions to run command line applications.

For further information, email bioinformatics-training@nullunimelb.edu.au.