dennyzen / vcf-toolkit Goto Github PK

Toolkit for benchmarking, merging, and annotating Structural Variants

📚 WIKI page has detailed documentation.
📈 See Updates on new versions.
📝 Read our Papers (#1, #2) to learn more.

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.

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 -o output_dir/

• bench - Performance metrics from comparison of two VCFs
• collapse - Collapse possibly redundant VCF entries
• anno - Add SV annotations to a VCF
• consistency - Consistency report between multiple VCFs
• vcf2df - Turn a VCF into a pandas DataFrame
• segment - Normalization of SVs into disjointed genomic regions
• stratify - Count variants per-region in vcf
• divide - Divide a VCF into independent shards
• phab - Harmonize variant representations using MSA
• refine - Automated bench result refinement with phab

All documentation about Truvari is on the WIKI. Additional information about using Truvari can be found in Discussions