nf-core/variantbenchmarking is a bioinformatics pipeline that …

  1. Standardization of SVs in test VCF files
  2. Normalization of SVs in test VCF files
  3. Normalization of SVs in truth VCF files
  4. SV stats and histograms
  5. Germline benchmarking of SVs
  6. Somatic benchmarking of SVs
  7. Final report and comparisons



If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Supported SV callers: Manta, SVaba, Dragen, Delly, Lumpy .. Available Truth samples: HG002, SEQC2

Now, you can run the pipeline using:

nextflow run nf-core/variantbenchmarking \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters;

see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.


nf-core/variantbenchmarking was originally written by

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don’t hesitate to get in touch on the Slack #variantbenchmarking channel (you can join with this invite).


An extensive list of references for the tools used by the pipeline can be found in the file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.