The EAGER pipeline uses several tools and methods in order to process data. The following list contains all tools and methods with respective links to the corresponding webpages. For licencing information regarding these methods and tools, please see the respective web pages.

  • FastQC
  • FastXTools
  • BWA/BWAMem
  • Samtools
  • Bowtie 2
  • Stampy
  • Preseq
  • Picard-Tools
  • QualiMap
  • mapDamage
  • Genome Analysis Toolkit (GATK)
  • schmutzi

The EAGER pipeline is available free of charge for academic purposes. The pipeline is available under GPLv3 (see source code on GitHub, too). For more information see the Docker Image Installation Instructions.

Important Licencing Information

The GATK is licensed by the Broad Institute and is made available to academic users of the EAGER pipeline described at for non-commercial research use only. The full text of the GATK license is available at For more information about GATK, please visit the GATK website at

GATK documentation resources and support

General GATK documentation can be found at on the GATK website at Users of this pipeline are welcome to ask GATK-related questions and report problems that are not specific to this pipeline in the GATK forum at