An Introduction to the Analysis of the Next-generation Sequencing Data [EL019]

Course highlights

EC points


Start date


End date


Course days

Monday to Friday


Prof. Fernando Rivadeneira, Jeroen van Rooij, Robert Kraaij, Carolina Medina-Gomez, Dina Vijonovi?, Haojie Lu, Vid Prijatelj, Constanza Vallerga, Vivi Zhou

Course fee

€ 945


Erasmus MC, Rotterdam NL




  • Genetic Epidemiology


How to apply

Detailed information about this course:


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.

See 'how to apply' for the course registration period.

Participant profile

Clinical researchers, clinical epidemiologists, molecular biologists, bioinformaticians and biostatisticians aspiring to run sequencing-based data analyses by themselves, or work with next-generation sequencing data and want to know how this is typically created. Some affinity with scripts and/or genetics is suggested.


Assignment(s), Attendance

Reduction on fees

PLEASE NOTE: This does not apply to the fee of the research master programmes (120 EC points)

No fees are charged for  Erasmus MC PhD candidates, provided they have an account in Hora Finita, the Erasmus University PhD registration system. When submitting the application, you can state that someone else pays your tuition fee.

In case of cancellation or no show, the cancellation policy applies based on the full course fee.


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

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