Hands-On introduction to NGS variant analysis


Using a full publicly available chromosome read-set from one of the 1000 genome sample:
  • ​Perform a complete analysis workflow including QC, read mapping, read coverage analysis, and variant calling against the human reference genome.
  • Use GenePattern and open source software to evaluate each step of a classical NGS variant workflow and feel the complexity of the task.
  • Quickly compare the obtained results with gold standard public data
The skills acquired during this session should allow participants understand what variant calling implies. Note that the more powerful approaches using command line (previous year sessions) will not be covered in this training.


This training gives an introduction to the use of several popular NGS analysis software packages under the GenePattern Graphical interface.



Skills required to follow this training include basic knowledge of Illumina NGS read structure. People who lack knowledge of Illumina reads should follow the 'Introduction to the analysis of NGS data' trainingDepending on the number of participants (max 20), it might be that you have to share the laptop with one other participant but you can also choose to bring your own laptop for this training session.​

Topics NOT covered in this session

  • similar workflow(s) using unix operative system and the command-line approach.​
  • ​similar workflow(s) using commercial products like the 'CLC genomics workbench'
  • similar workflow(s) using the free Galaxy GUI (although perfectly doable using the acquired knowledge)
  • variant analysis at multi-genome level & GWAS (<- advanced computing and statistical expertise required).
  • structural variant analysis (large indels, translocations, CNV) as being too complex with no all-in-one tool available.


9 and 16 November 2018, from 9h30 to 17h00


Park Inn by Radisson Leuven
Martelarenlaan 36
3010 Leuven


Stéphane Plaisance and Guy Bottu

Training material:

Registration is closed.

Registration start date:

12 September 2018

Registration end date:

26 October 2018