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

Course highlights

EC points

1.4

Start date

28-02-2022

End date

04-03-2022

Course days

Monday to Friday

Faculty

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

Course fee

€ 910

Location

Erasmus MC, Rotterdam NL

Level

Introductory

Disciplines

  • Genetic Epidemiology

Application

How to apply

Detailed information about this course:

Description

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.

Assessment

Assignment(s), Attendance


Reduction on fees

PLEASE NOTE THIS DOES NOT APPLY TO THE RESEARCH MASTERS (120 EC points)

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.

 

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.