DNA Variant Calling Workshop
How to call genomic variations and uncover their effects

Advance your research and uncover genomic variations and their effects.

In a nutshell

  • Understand NGS technologies, data formats and algorithms
  • Learn essential computing skills for NGS bioinformatics
  • Use bioinformatics tools like GATK to predict variants
  • Uncover the effects of relevant variants

21 - 23 September 2016
Berlin, Germany

The purpose of this workshop is to predict single nucleotide variations (SNVs) using Next-Generation Sequencing (NGS). Advantages and disadvantages of current tools and their implications on downstream analyses will be discovered. We will use different variant calling tools including the Genome Analysis Toolkit (GATK) and discuss best practices for variant discovery. The participants will be trained on analyzing their own NGS data, finding potential SNVs therein and finally perform downstream analyses including the prediction of variant effects, analyses of affected pathways, associations of detected SNPs to diseases, etc. In the course we will use a real-life DNA-seq dataset from the current market leader illumina.

All workshop attendees will be enabled to perform important first tasks of NGS data analysis themselves. The course layout has been adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this new and fast evolving research topic.

Check our new course layout.

Get trained by experts

Our trainers have a proven record of academic and/or industrial experience in NGS data analysis. Because up-to-date expert knowledge is needed to answer your questions and know what is important in the field.

Open source NGS tools

We only use open source tools that are free to use. We try to showcase and compare different tools (e.g. NGS mappers), since not every software fits with every task/question.

Learn effectively with well-curated materials

For a optimal learning experience we carefully prepare our learning materials and example data. All materials, tools and results created during the course are for take home with you.

This workshop has been redesigned and adapted to the needs of beginners in the field of NGS bioinformatics and comprises this three course modules:

  1. NGS for beginners:
    This module will introduce the essential tools and file formats required for NGS data analysis. It helps to overcome the first hurdles when entering the field of variant calling. Different methods of NGS will be explained, the most important notations will be given and first analyses will be performed.
  2. Introduction to variant calling:
    This day covers essential knowledge for understanding the statistics behind relevant variant calling tools and theirpros and cons. You will use different variant calling tools and learn how to interpret and compare their output.
  3. Uncover effects of relevant variants:
    You will learn how to filter for relevant SNVs. You will identify the genomic sequence context (intergenic, intron, exon...) of SNPs. You will learn how to predict functional consequences of a SNP to the affected proteins (synonymous VS non-synonymous), affected pathways (GO-term Analysis) and affected individuals (disease associated SNPs).

Detailed Course Program

NGS for beginners

  • Introduction to sequencing technologies from a data analysts view
  • Raw sequence files (FASTQ format)
  • Preprocessing of raw reads: Idea of adapter clipping and quality trimming
  • Mapping output (SAM/BAM format)

Introduction to variant calling

  • Introduction to variant calling and its statistics
  • Running the Genome Analysis Toolkit (GATK) and other variant calling tools
  • Variant calling output (VFC format)
  • Comparing the results of the different tools
  • Visualisation of SNPs in a genome browser

Uncover effects of relevant variants

  • Position within genome (intergenic, intron, exon...)
  • Effect on protein function (synonym VS non-synonym)
  • Effect on pathways(GO-Term analysis)
  • Effect on individuals (disease associations...)


Dr. Jörg Linde (Hans Knöll Institute)
Jörg analyses Next-Generation Sequencing data of human pathogens and their host. He has developed pipelines for dual-RNASeq data and SNP-calling analysis. Jörg is interested in the consequences of gene expression changes and genomic variations to host-pathogen interactions.

Dr. Rina Ahmed (CCR Bio-IT)
Rina is a bioinformatician by training and specialized in the field of Next-Generation-Sequencing in 2010. During her PhD work on microRNA genes and their evolution in nematodes she was involed in the development of the barcode and adapter removal tool flexbar. Rina has developed NGS data analyses pipelines for small RNA-Seq and DNA resequencing data.

Dr. Mario Fasold (CCR Bio-IT)
Mario works in the analysis of microarray data since 2007 and developed several bioinformatics tools such as the Bioconductor package AffyRNADegradation and the Larpack program package. Since 2011 he specialized in the field of NGS data analysis and helped analysing sequecing data of several large consortium projects.


  • basic understanding of molecular biology (DNA, RNA, gene expression, PCR, ...)
  • For the Introduction to NGS Data Analysis and downstream courses: basic linux & bioinformatics knowledge (shell usage, common commands and tools). You should be familiar with the commands covered in the Learning the Shell Tutorial

The target audience is biologists or data analysts with no or little experience in analyzing DNA-Seq data.

  •   Course materials
  •   Catering during the workshop
  •   Conference dinner
  •   High-performance workstations (no laptop needed)
  •   USB-Stick for taking home results and analysis


Location: PC-College, Stresemannstra├če 78, 10963 Berlin, Germany
Language: English
Available seats: 20 (first-come, first-served)

Travel expenses and accommodation are not covered by the registration fee.

Travel Information - Berlin

Key dates

Opening Date of Registration: 01 March 2016
Closing Date of Registration: 01 September 2016
Workshop:21 - 23 September 2016 (9 am - 5 pm)


"Very valuable workshop which improved my bioinformatics understanding a lot and provided interesting aspects, I will put more focus on while analyzing our own data." Corinna Streitner, KWS Saat AG, Germany

"The workshop provided a great introduction into the analysis of NGS data for me as a wet lab biologist. The one day introduction into Linux was an absolute asset. Thanks to the course, I now feel comfortable both to discuss my NGS analysis needs with a bioinformatician more competently, but also to take first steps in NGS analyses myself." Tobias Schmid, Goethe-University Frankfurt, Germany.

"Good resume of the last technologies and applications. Definitly will improve the comunication with our bioinformatics colleagues for perfom the proper analysis and understanding of the data. Thanks for an intensive but nice course." Susana Gonzalez Fernandez-Nino, Bayer Crop Science, Germany

When you register for this workshop you are agreeing with our Workshop Terms and Conditions. Please read them before you register.

Any Questions? Please feel free to contact our events team.

ecSeq GmbH
Brandvorwerkstr. 43
04275 Leipzig
Email: events@ecSeq.com