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  • Walid Gharib
  • Irene Keller
  • Geert van Geest

License: CC BY-SA 4.0

Copyright: SIB Swiss Institute of Bioinformatics


  • This website
  • Zoom meeting (through mail)
  • Google doc (through mail)
  • Slack channel

Learning outcomes

After this course, you will be able to:

  • Understand important aspects of NGS and read alignment for variant analysis
  • Perform a read alignment ready for variant analysis
  • Perform variant calling according to GATK best practices
  • Perform a variant annotation

Learning experiences

This course will consist of lectures, exercises and polls. During exercises, you are free to discuss with other participants. During lectures, focus on the lecture only.


Each block has practical work involved. Some more than others. The practicals are subdivided into chapters, and we’ll have a (short) discussion after each chapter. All answers to the practicals are incorporated, but they are hidden. Do the exercise first by yourself, before checking out the answer. If your answer is different from the answer in the practicals, try to figure out why they are different.

Asking questions

During lectures, you are encouraged to raise your hand if you have questions (if in-person), or use the Zoom functionality (if online). Find the buttons in the participants list (‘Participants’ button):

Alternatively, (depending on your zoom version or OS) use the ‘Reactions’ button:

A main source of communication will be our slack channel. Ask background questions that interest you personally at #background. During the exercises, e.g. if you are stuck or don’t understand what is going on, use the slack channel #q-and-a. This channel is not only meant for asking questions but also for answering questions of other participants. If you are replying to a question, use the “reply in thread” option:

The teacher will review the answers, and add/modify if necessary. If you’re really stuck and need specific tutor support, write the teachers or helpers personally.

To summarise:

  • During lectures: raise hand/zoom functionality
  • Personal interest questions: #background
  • During exercises: #q-and-a on slack