Variant detection using Galaxy

This 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.
 

 

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

Syllabus

  • 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

For more information contact training@qfab.org