NGS - Genome Variant Analysis

29 - 30 April 2019
Cancellation deadline:
15 April 2019
Walid Gharib
Omics data analysis
0.5 credits
Applications are closed because the course is full with a long waiting list or has just passed. to receive notification when a new course is scheduled.

Next course(s):
08 - 09 Dec 2020 Streamed
30 - 31 Mar 2021 Streamed
16 - 17 Sep 2021 Streamed
24 - 25 Mar 2022 Streamed
26 - 27 Sep 2022 Bern
20 - 21 Feb 2023 Bern
23 - 24 Nov 2023 Streamed

This course is over subscribed. You can still add your name to the waiting list by applying using the button at the bottom of this page. You will only be contacted if a place becomes available.


Among other genomic applications, Whole genome sequencing “WGS”, Whole Exome Sequencing “WES” and RNA sequencing are used for the detection of genomic variants. On a genomic scale, variations manifest in the form of Single Nucleotide variants “SNVs”, insertions and deletions “Indels”, copy number variants “CNVs” or chromosomal rearrangements and are generally detected by comparing the sequencing data to a reference. The detection of genetic variations is a major interest in various genomics disciplines applications spanning from ecology and evolution research to Inherited disease discovery/diagnostics and precision oncology.

This 2 days course targets biologists and computational biologists. We will mainly focus on the detection of germline mutations by following the GATK best practices; we will also make use of other tools especially for the annotation part.


This course is intended for life scientists who are already familiar with general concepts of NGS technologies.

Learning objectives

At the end of the course participants should be able to:

  • Validate mapping output files
  • Gather input information from public databases
  • Perform local realignment to reduce false discovery
  • Map quality control
  • Call variants based on GATK best practices
  • Annotate Variants


Knowledge / competencies:

Participants should have knowledge in Next generation sequencing techniques, pre-mapping quality control, filtering and mapping to reference genome. Participants should have a basic understanding of working with command line tools on Linux or Windows-based operating systems. If you do not feel comfortable with UNIX commands, please take our UNIX fundamentals e-learning module.


Participants should bring their own computers and chargers.


This course is over subscribed. You can still add your name to the waiting list by applying using the button at the bottom of this page. You will only be contacted if a place becomes available.

The registration fees are 120 CHF for academics and 600 CHF for companies.

Deadline for registration and free-of-charge cancellation is set to April 15. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to this and other general conditions, available here.

You will be informed by email of your registration confirmation.


Universität Bern, Hochschulstrasse 4 (main building of the University of Bern), classroom 331, 3. OG West.


Day 1 - 9h15 to 17h


  • Introduction to Variant discovery
  • Fetching sequencing data using Eutilities and SRA tools
  • Indexing references & mapping/sorting/indexing alignment


  • Differences in workflows between DNA-seq (WGS, WES) and RNA-seq
  • Marking duplicates
  • Realignment around SNPs and indels

Day 2 - 9h15 to 17h


  • Base quality score recalibration
  • Calling the variants (single and multiple samples)
  • Joint genotyping


  • Variant filtering
  • Variant annotation
  • Installing used software for a local use
  • Optional exam

Additional information

The course will be taught by Walid Gharib

Coordination: Walid Gharib and Patricia Palagi

We will recommend 0.5 ECTS credits for this course (given a passed exam - optional - at the end of the session). 

You are welcome to register to the SIB courses mailing-list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

For more information, please contact