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sv-callers

Highly portable parallel workflow to detect structural variants in cancer genomes.

30
mentions
4
contributors

Cite this software

What sv-callers can do for you

  • Enables comprehensive detection of structural variants (SVs) by combining multiple tools
  • Supports both single-sample (germline) and paired-sample (somatic) SV analyses
  • Makes the analyses scalable and easily portable across HPC clusters (e.g., using GridEngine, Slurm etc.) or compute clouds
  • 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.

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Keywords
Programming languages
  • Python 94%
  • Shell 6%
License
</>Source code

Participating organisations

Netherlands eScience Center
University Medical Center Utrecht

Reference papers

Mentions

Portable HPC workflows with Snakemake, Conda, and Xenon

Author(s): Jurriaan H. Spaaks
Published in 2018

Contributors

LS
Luca Santuari
University Medical Center Utrecht
Stefan Verhoeven
Stefan Verhoeven
Netherlands eScience Center

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