Cancer variant analysis

COURSE INTRODUCTION

Flavio Lombardo

2025-12-12

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 abide to the ELIXIR code of conduct during the course

  • If you witness unacceptable behaviour that can’t be dealt with with the people involved in this course, contact the COC oversight group

  • More info: here

Etiquette
ELIXIR Code of Conduct Principles

Trainers/organizers/Helpers

  • Gregoire Rossier: Training coordinator at SIB
  • Diana Marek: Training coordinator at SIB
  • Geert Van Geest: Training Project Manager at SIB
  • Flavio Lombardo: Computational Biologist at the University Hospital Basel
  • Deepak Tanwar: Bioinformaticis Specialist and Trainer at SIB
  • Aparna Pandey: Bioinformatic Analyst at Interfaculty Bioinformatics Unit, University of Bern

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

Learning experiences

  • Lectures

  • Polls + quiz questions

  • Exercises

Communication

Asking questions

  • During lectures: zoom functionality – but the chat will be ignored

  • During exercises: #q_and_a channel on Zulip
    • You can add a topic for your question, this will open a new conversation-topic.

Zulip thread
Zulip channels

Tell us about yourself:

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

…And consider the social channel in Zulip!