README.md

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Toolkit for benchmarking, merging, and annotating Structrual Variants

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

Installation

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.