Practical Somatic Variant Analysis in Cancer Genomics

COURSE INTRODUCTION

Dr. Flavio Lombardo

2026-04-27

Course etiquette

Etiquette

Etiquette

Video on when possible

Use your first and last name as your Zoom ID

  • Right-click on yourself > Rename..

Mute when not speaking

Code of conduct

  • Learning can only be done in a safe environment

  • We expect all participants to treat each other with respect and professionalism

  • Be considerate and collaborative — everyone is here to learn

  • If you witness or experience unacceptable behaviour, please contact the instructor directly

Code of Conduct

Instructor

  • Dr. Flavio Lombardo: Computational Biologist at the University Hospital Basel / University of Basel

The views and opinions expressed in this course are my own and do not necessarily reflect those of my employer.

Learning outcomes

  • Understand the difference between germline and somatic variants and the implication of computational analysis

  • Perform a somatic variant analysis on a paired sample (tumor – normal) with GATK4

  • Perform a somatic variant annotation with VEP and use the results to filter possible high-impact mutations in the cancer genome

Tell us about yourself:

  • Name and affiliation
  • Research area / current project
  • Experience with variant analysis
  • What you hope to learn from this course

…And feel free to connect with fellow participants on Slack!

Attribution

This course builds upon materials originally developed for SIB Swiss Institute of Bioinformatics by Flavio Lombardo and Geert van Geest, with additional inspiration from the Precision Medicine Bioinformatics course by the Griffith Lab.

License: CC BY 4.0