A portable and scalable bioinformatics workflow for detecting structural variants in whole-genome sequencing data.

151 commits | Last update: May 22, 2018

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What sv-callers can do for you

  • Enables portable genome-wide detection of SVs using different HPC systems (e.g. GridEngine- or Slurm-based clusters)
  • Provides a command-line interface for executing state-of-the-art SV callers in a parallel workflow
  • It's easy to install, configure, deploy and extend

This Snakemake-based workflow combines several state-of-the-art tools (i.e. Manta, DELLY, LUMPY and GRIDSS) for detecting structural variants (SVs) in whole genome sequencing data. The workflow is easy to use and to deploy on any Linux-based machine. In particular, the workflow supports automated software deployment, easy configuration and addition of new analysis tools as well as enables to scale from a single computer to different HPC clusters with minimal effort.

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  • High performance computing
  • Workflow technologies
Programming Language
  • Python
  • Java
  • Apache-2.0
Source code

Participating organizations


  • Arnold Kuzniar
    Netherlands eScience Center
  • Stefan Verhoeven
    Netherlands eScience Center
  • Jason Maassen
    Netherlands eScience Center
Contact person
Arnold Kuzniar
Netherlands eScience Center