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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.

Installation

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 setup.py 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.

https://www.spiralgenetics.com

Project details


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