NGS - Genome Variant Analysis

11-12 June 2026

Dre Diana Marek, SIB

Dr Geert van Geest, UNIBE and SIB

The detection of genetic variation is of major interest in various disciplines spanning from ecology and evolution research to inherited disease discovery and precision oncology. Next generation sequencing (NGS) methods are very powerful for the detection of genomic variants. Thanks to its throughput and cost-efficiency it enables the detection of a large number of variants in a large number of samples. In this two-day course we will cover the steps from read alignment to variant calling and annotation. We will mainly focus on the detection of germline mutations by following the GATK best practices. The training materials for this course are in its dedicated GitHub page. Learning objectives: At the end of the course participants should 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. Prerequisite: This course is intended for life scientists who are already familiar with general concepts of NGS technologies and want to expand their knowledge and skills on variant analysis.

Overview
The detection of genetic variation is of major interest in various disciplines spanning from ecology and evolution research to inherited disease discovery and precision oncology. Next generation sequencing (NGS) methods are very powerful for the detection of genomic variants. Thanks to its throughput and cost-efficiency it enables the detection of a large number of variants in a large number of samples. In this two-day course we will cover the steps from read alignment to variant calling and annotation. We will mainly focus on the detection of germline mutations by following the GATK best practices. The training materials for this course are in its dedicated GitHub page.

Audience
This course is designed for PhD students, postdoctoral and other researchers in the life sciences from both academia and industry who are already familiar with general concepts of NGS technologies and want to expand their knowledge and skills on variant analysis.

Learning objectives
At the end of the course participants should 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

Prerequisites Knowledge / competencies:
Participants should have knowledge in NGS techniques, quality control and alignment to a reference genome. Participants should have a basic understanding of working with command line tools on Unix-based systems. You can test your skills with Unix with the quiz here. If you do not feel comfortable with UNIX commands, please take our Unix fundamentals e-learning module.

Technical:
Participants should have their own computers.

Location
This course will take place at the University of Basel. It will start at 9:00 and end around 17:00. Precise information will be provided to the participants in due time.

Schedule
The schedule and course materials are in the dedicated GitHub page.

University of Basel

If you need housing for the night inbetween, please contact your doctoral program prior to the reservation.

Staromics (4 places)
EE (4 places)
Microbiology (6 places)
MPS (2 places)

Usually 2 months before the course on this link : https://www.sib.swiss/training/course/20260611_NGSGV, while registering mention that you are part of StarOmics

(Please register also on the CUSO website in order to claim your travel costs). Registration deadline: 28 May 2026

14