Free

Introduction to Variant Calling with Galaxy & Genomics Virtual Laboratory

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Location

Melbourne Bioinformatics Boardroom

187 Grattan st

Ground floor

Parkville, VIC 3010

Australia

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Event description
Learn the process of SNP and Indel detection using Galaxy, an intuitive and highly visual online tool.

About this Event

Overview

Presenter - Khalid Mahmood

This tutorial is designed to introduce the tools, datatypes and workflow of variant detection. We will align reads to the genome, look for differences between reads and reference genome sequence, and filter the detected genomic variation manually to understand the computational basis of variant calling.

In this tutorial we cover the concepts of detecting small variants (SNVs and indels) in human genomic DNA using a small set of reads from chromosome 22.

Learning objectives

By the end of this training, participants will be able to:

  • Work with the FASTQ format and base quality scores
  • Align reads to generate a BAM file and subsequently generate a pileup file
  • Call simple variants (SNVs and indels) using a variant caller
  • Visualise BAM files using the Integrative Genomics Viewer (IGV) and identify likely SNVs and indels by eye

Prerequisites and Requirements

This workshop requires does not require any previous experience but familiarity with Galaxy or completion of “Introduction to Galaxy” workshop is recommended.

This is a hands-on workshop and attendees must bring their own laptops to the workshop with the following software preinstalled:

Most workshops are FREE for all researchers and students from the University of Melbourne and its affiliated research institutes. For details of charges for external participants please see the Melbourne Bioinformatics Training page.

Building Access

Please note that the venue for the workshop, 187 Grattan St (Building 257), does not have an accessible entrance. There are a number of steps leading from street level up to the ground floor entrance and there are no accessible toilets available in the building.

If you have any access requirements in order to participate in this workshop, please contact the workshop organiser (bioinformatics-training@unimelb.edu.au) as soon as possible to discuss your requirements further.

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Date and Time

Location

Melbourne Bioinformatics Boardroom

187 Grattan st

Ground floor

Parkville, VIC 3010

Australia

View Map

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