Structural variant comparison tool for VCFs
Project description
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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 3.6+ 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.
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