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Structural variant toolkit for benchmarking, annotating and more for VCFs

WIKI page has detailed documentation. See Updates on new versions.


Truvari uses Python 3.7 and can be installed with pip:

  pip install Truvari 

PyPi has a history of all versions available. Pip installs all requirements EXCEPT external tools needed for running some annotations. See anno for details.

To build and install Truvari from scratch:

  python -m pip install --upgrade pip setuptools wheel
  python sdist bdist_wheel
  pip install dist/Truvari-<version>.tar.gz

Where <version> is which version you just built.

See tags/ for a list of all available versions.

Quick Start

Each sub-command contains help documentation. Start with truvari -h to see available commands.

The current most common Truvari use case is for structural variation benchmarking:

  truvari bench -b base.vcf.gz -c comp.vcf.gz -f reference.fasta -o output_dir/

Truvari Commands

  • bench - Performance metrics from comparison of two VCFs
  • stats - Basic SV relevant VCF stats
  • consistency - Consistency report between multiple VCFs
  • anno - Add SV annotations to a VCF
  • collapse - Collapse possibly redundant VCF entries
  • truv2df - Turn a Truvari directory's VCFs into a pandas DataFrame

More Information

Find more details and discussions about Truvari on the WIKI page.

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