Variant calling using GATK4 command line workflow

Variant calling using GATK4 command line workflow

Lead trainer:

Khalid Mahmood (Melbourne Bioinformatics, The University of Melbourne)

Target audience:

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

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

Cloud computer

Eligibility:

This Free workshop is available to staff and students at The University if Melbourne and its affiliated institutes.

You must register for this event using an affiliated institutional email address or your registration may be cancelled.

Prerequisites and Requirements

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).

Required:

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 July 17th, 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.

This is an in person hands-on workshop and attendees must bring their own computers (laptop chargers also recommended). No software needs to be installed for this workshop and no programming experience is necessary. The following is required:

• Access to internet via uniwireless or Eduroam
• Web browser (Firefox or Chrome recommended)
• Participants should register for a Galaxy Australia account using their institutional email address

Access

If you require any further information, or have any access requirements in order to participate in this workshop, please contact us as soon as possible to discuss your requirements:

We recommend that following our eventbrite page if you wish to be alerted when we release new workshops for registrations. If you require any further information, please contact Melbourne Bioinformatics at:

bioinformatics-training@unimelb.edu.au