Variant detection using Galaxy

2 March 2017, Brisbane

This QFAB workshop will cover the concepts of detection small variants, including SNPs and small indels, from next-generation sequencing data. You will use and compare a number of popular variant detection tools, visualise variants using a genome browser, and annotate SNPs for predicted biological effects.

The workshop will all be based in Galaxy, a platform that provides a simple and user-friendly interface to bioinformatics tools.

Recommended Participants:

Biologists and other life scientists planning to work with next-generation sequencing data for small variant detection. Participants must bring their own laptops with wireless network capability.


• Access and use of the Galaxy bioinformatics analysis platform
• Quality control and filtering of next-generation sequencing data
• Next-generation sequencing read mapping
• Visualisation of mapped reads with the Integrative Genomics Viewer
• Use of and comparison of software applications to call genomic variants
• Filtering and screening protocols to generate lists of high-confidence SNPs
• Initial annotation of the predicted biological impact of identified variants

Learning Objectives:

• Perform QC evaluation and filtering on next-generation sequencing data
• Select and use relevant variant detection software and apply appropriate quality filters to screen variants
• View variant and sequence data using the Integrative Genomics Viewer (IGV)
• Carry out preliminary functional annotation of predicted variants.

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