truvari 5.4.0
Structural variant comparison tool for VCFs
License: MIT
Requires Python: >=3.8

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![Logo](https://raw.githubusercontent.com/ACEnglish/truvari/develop/imgs/BoxScale1_DarkBG.png)  
Toolkit for benchmarking, merging, and annotating Structural Variants

📚 [WIKI page](https://github.com/acenglish/truvari/wiki) has detailed user documentation.  
🛠️ [Developer Docs](https://truvari.readthedocs.io/en/latest/) for the truvari API.  
📈 See [Updates](https://github.com/acenglish/truvari/wiki/Updates) on new versions.  
📝 Read our Papers ([#1](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02840-6), [#2](https://rdcu.be/dFQNN)) to learn more.

## 💻 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](https://github.com/acenglish/truvari/wiki/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.fa -o output_dir/
```

Find more matches by harmonizing phased variants using refine:
```
   truvari refine 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
```

## 🧬 Truvari Commands

 - [bench](https://github.com/acenglish/truvari/wiki/bench) - Performance metrics from comparison of two VCFs
 - [collapse](https://github.com/acenglish/truvari/wiki/collapse) - Collapse possibly redundant VCF entries
 - [refine](https://github.com/ACEnglish/truvari/wiki/refine) - Automated bench result refinement with phab
 - [anno](https://github.com/acenglish/truvari/wiki/anno) - Add SV annotations to a VCF
 - [phab](https://github.com/ACEnglish/truvari/wiki/phab) - Harmonize variant representations using MSA
 - [consistency](https://github.com/acenglish/truvari/wiki/consistency) - Consistency report between multiple VCFs
 - [vcf2df](https://github.com/acenglish/truvari/wiki/vcf2df) - Turn a VCF into a pandas DataFrame
 - [segment](https://github.com/acenglish/truvari/wiki/segment) - Normalization of SVs into disjointed genomic regions
 - [stratify](https://github.com/acenglish/truvari/wiki/stratify) - Count variants per-region in vcf
 - [divide](https://github.com/ACEnglish/truvari/wiki/divide) - Divide a VCF into independent shards
 - [ga4gh](https://github.com/ACEnglish/truvari/wiki/ga4gh) - Consolidate benchmarking result VCFs

## 🔎 More Information

All documentation about Truvari is on the [WIKI](https://github.com/acenglish/truvari/wiki). Additional information about using Truvari can be found in [Discussions](https://github.com/ACEnglish/truvari/discussions)