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BIO392 - Bioinformatics of Sequence Variation

This is a repository for materials related to the BIO392 Bioinformatics of Sequence Variation introductory course at the University of Zürich. The course takes place in each Autumn semester (September/October).


One of the fastest growing areas of bioinformatics is in the analysis, warehousing and representation of genomic and protein sequence variants, particularly with view on the use of molecular data in personalised health and biomedical applications in general. This course will engage participants to explore common data formats, online resources and analysis techniques, with a focus on human genome variation data.

Practical Information

Technical requirements

  • the course lab is equipped with iMacs - however, feel free to use your personal machines (which may anyway be advantageous for "home office" work)
  • you will need to have / create a Github account (though this is also addressed at the beginning of the course)



UZH BIO392 HS22 - Day 14
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Genomic Privacy and Q & A

UZH BIO392 HS22 - Day 13

Michael Baudis

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Survival Analysis Exercise & Discussion

UZH BIO392 HS22 - Day 12
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Survival Analysis Exercise & Discussion

UZH BIO392 HS22 - Day 11
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From Sequence to Variants & Survival Analysis Introduction

UZH BIO392 HS22 - Day 10
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Survival as a Measure in Cancer Genomics? Also: Cancer Classifications

UZH BIO392 HS22 - Day 09

Michael Baudis

This day provides some notes about the submitted notes, introduction to Kaplan-Meier survival analysis concepts and classification systems used to describe cancer types and clinical apperances. Continue reading

Sequences Repeating Themselves - STRs et al.

UZH BIO392 HS22 - Day 08
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Sequence Search with BLAST & Clinical Variant Interpretation Resource

UZH BIO392 HS22 - Day 07


  • introduction of BLAST

  • excercise on using BLAST


get familiar with some clinical variant annotation resources.

  • introduction of ClinVar and ClinGen

  • exercise on using ClinVar and ClinGen

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Online Resources for Human Genomic Variations & Introduction to CNVs

UZH BIO392 HS22 - Day 06
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Genome Analysis Technologies

UZH BIO392 HS22 - Day 05

Michael Baudis

Some information about genomic analysis technologies, file formats ...

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Genomic File Formats, 1000 genomes project

UZH BIO392 HS22 - Day 04

Izaskun Mallona (email: izaskun.mallona at

Morning (on site, 9 am)

We will have a lecture and run a set of exercises (on site).

  • Overview of the standard genomics data formats
  • SAM
  • BED
  • GFF
  • VCF
  • Basic file processing for bioinformatics
  • wc, grep, awk
  • Exercises
  • Project

Afternoon (on site or online)

Exercises and project.

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Terminal, Unix & Files

UZH BIO392 HS22 - Day 03

Izaskun Mallona (email: izaskun.mallona at

Morning (on site, 9 am)

We will have two lectures and several sets of exercises (on site).

  • Unix + genomic formats lectures (exercises 1-4)
  • Unix and genomic formats exercises (5-14)

Afternoon (on site or online)

We will run the SIB Unix course using a Web browser. We encourage you to run the exercises of the course in a terminal of your own; either on a GNU/Linux or MacOS; or with a Web browser-based emulator of your choice, like cocalc. Continue reading

Github, Terminal & Editors

UZH BIO392 HS22 - Day 02

The second day of the "Bioinformatics of Sequence Variation" course, with some inroduction and setups of Github, Terminal & Editors.

  • 9:00 - 10:00: Introduction of Github things.
  • 10:00 - 11:00: Github exercise: create user specific directories & upload/edit test files using Markdown.
  • 11:00 - 12:00: Introduction to different interfaces eg atom, pycharm (lecture), editor setup exercise.

  • 13:00 - 14:00: Get familiar with R (lecture).

  • 14:00 - 15:00: Literature (genome variant review papers).
  • 15:00 - 16:30: Task: Answer the questions of literature review session and provide some notes (1-2 pages total) in a doc posted on Github (.md)
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Introduction & Technicalities

UZH BIO392 HS22 - Day 01

The first day of the "Bioinformatics of Sequence Variation" course (afternoon only) starts with a general introduction to the course's topics, timeline and procedures.

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