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Structural variant toolkit for benchmarking, annotating and more for VCFs

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

Installation

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 setup.py 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.

https://www.spiralgenetics.com


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