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/
Find more matches by harmonizing phased varians using refine:
truvari refine -R -U -r reference.fa --regions output_dir/candidate.refine.bed output_dir/
Use Truvari's comparison engine to consolidate redundant variants in a merged multi-sample VCF:
bcftools merge -m none sampleA.vcf.gz sampleB.vcf.gz | bgzip > merge.vcf.gz
tabix merge.vcf.gz
truvari collapse -i merge.vcf.gz -o truvari_merge.vcf
- bench - Performance metrics from comparison of two VCFs
- collapse - Collapse possibly redundant VCF entries
- refine - Automated bench result refinement with phab
- anno - Add SV annotations to a VCF
- phab - Harmonize variant representations using MSA
- 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
- ga4gh - Consolidate benchmarking result VCFs
All documentation about Truvari is on the WIKI. Additional information about using Truvari can be found in Discussions