An Introduction to the Analysis of the Next-generation Sequencing Data [GE13]

Course highlights

EC points




Course days

Monday to Friday


To be announced

Course fee

€ 910


Erasmus MC, Rotterdam NL




  • Genetic Epidemiology


How to apply

Detailed information about this course:


In 2021 this course will not be offered as a separate course - a compact version will be merged with the course GE03 Advances in Genome-Wide Association Studies.

This course provides an introduction to working with Next-Generation Sequencing (NGS) data. It targets individuals who have access to NGS data and want to learn how to work with this data and what the possibilities and limitations of NGS are. Lectures will be complemented with practical sessions in which the student will gain hands-on experience with various tools and techniques.Subjects that will be covered include:

  • NGS: an introduction to methodology and techniques;
  • Basic statistics of NGS data, e.g. coverage;
  • Aligning the sequence reads;
  • Calling sequence and structural variants;
  • Dealing with various file formats (samtools, VCFtools, GATK);
  • Annotating sequence and structural variants;
  • Evaluating functional effects of the genetic variants on proteins;
  • Conversion to other formats;
  • Single variant and Collapsed genotype analyses with various tools (e.g. seqMeta, RAREMETAL and RVtest);
  • Finding variants with recessive effects and compound heterozygosity;
  • Search for rare variants in families and population based studies for complex phenotypes;
  • Search for rare variants in Mendelian disorders, and
  • Imputation of sequence variants.


Written exam

Reduction on fees


No fees are charged for participation of Erasmus MC PhD candidates

Please note that in case of cancellation or no show, the cancellation policy applies based on the full course fee.

50% reduction on our fees for participating institutes of NIHES

This 50% reduction is offered to participants formally appointed at the departments or sections participating in NIHES.

University Medical Center Rotterdam/Erasmus University Rotterdam:

  • Department of Epidemiology
  • Department of Public Health
  • Department of Psychiatry, Section of Medical Psychology and Psychotherapy
  • Department of Child and Adolescent Psychiatry/Psychology
  • Department of Medical Informatics
  • Department of General Practice
  • Erasmus School of Health Policy & Management
  • Generation R

50% reduction on our fees for NIHES affiliated partners

This 50% reduction is offered to participants formally appointed at the following NIHES affiliated partners:

University Medical Center Rotterdam/Erasmus University Rotterdam, departments of:

  • Dermatology
  • General Paediatrics
  • Plastic and Reconstructive Surgery
  • Rehabilitation Medicine

UMIT, Department of Public Health, Health Services Research and Health Technology Assessment.

25% reduction on our fees for Erasmus MC employees

For participants formally appointed at all departments of Erasmus MC (except the departments mentioned above and Erasmus MC PhD candidates).

25% reduction for all (international) PhD students without formal appointment at Erasmus MC

Upon receipt of your application you will receive a request to upload proof of enrollment as a PhD student.