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Structural variant comparison tool for VCFs

Project description

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PyPI version pylint FuncTests coverage develop Downloads

Toolkit for benchmarking, merging, and annotating Structrual Variants

WIKI page has detailed documentation.
See Updates on new versions.
Read our Paper for more details.


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

  python3 -m pip install Truvari 

For details and more installation options, see Installation on the wiki.

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
  • divide - Divide a VCF into independent parts
  • segment - Normalization of SVs into disjointed genomic regions

More Information

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

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