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Highly portable parallel workflow for detecting structural variants in cancer genomes.

323 commits | Last update: June 21, 2019

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What sv-callers can do for you

  • Enables comprehensive detection of structural variants (SVs) using multiple tools
  • Supports both germline and somatic SV analyses
  • Makes the analyses scalable and easily portable to different HPC clusters (e.g., based on GridEngine, Slurm etc.) or compute clouds
  • Ensures efficient execution of jobs in parallel across cluster nodes
  • It's easy to use, deploy and extend with new tools

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.

Read more
  • High performance computing
  • Workflow technologies
  • Big data
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
  • Luca L Santuari
    University Medical Center Utrecht
Contact person
Arnold Kuzniar
Netherlands eScience Center