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Structural variant comparison tool for VCFs

Project description

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PyPI version pylint FuncTests coverage develop

Structural variant toolkit for benchmarking, annotating and more for VCFs

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


Truvari uses Python 3.6+ and can be installed with pip:

  python3 -m 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:

  python3 install

See tags/ for a list of all available versions.

See Development/docker for instructions on how to build and use a Truvari Docker container.

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
  • collapse - Collapse possibly redundant VCF entries
  • anno - Add SV annotations to a VCF
  • vcf2df - Turn a VCF into a pandas DataFrame
  • consistency - Consistency report between multiple VCFs

More Information

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

Project details

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Files for Truvari, version 3.0.0
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