Metadata-Version: 2.1
Name: Truvari
Version: 2.1.1
Summary: Structural variant comparison tool for VCFs
Home-page: https://github.com/spiralgenetics/truvari
Author: ACEnglish
Author-email: acenglish@gmail.com
License: MIT
Platform: UNKNOWN
Description-Content-Type: text/markdown
Requires-Dist: ACEBinf (>=1.0.2)
Requires-Dist: python-Levenshtein (==0.12.1)
Requires-Dist: progressbar2 (>=3.41.0)
Requires-Dist: pysam (>=0.15.2)
Requires-Dist: pyfaidx (>=0.5.5.2)
Requires-Dist: intervaltree (>=3.0.2)
Requires-Dist: joblib (>=0.14.1)
Requires-Dist: numpy (>=1.18.1)
Requires-Dist: pyfaidx (>=0.5.8)
Requires-Dist: pytabix (>=0.1)
Requires-Dist: bwapy (>=0.1.4)
Requires-Dist: pandas (>=1.0.5)


```
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╚══██╔══╝██╔══██╗██║   ██║██║   ██║██╔══██╗██╔══██╗██║
   ██║   ██████╔╝██║   ██║██║   ██║███████║██████╔╝██║
   ██║   ██╔══██╗██║   ██║╚██╗ ██╔╝██╔══██║██╔══██╗██║
   ██║   ██║  ██║╚██████╔╝ ╚████╔╝ ██║  ██║██║  ██║██║
   ╚═╝   ╚═╝  ╚═╝ ╚═════╝   ╚═══╝  ╚═╝  ╚═╝╚═╝  ╚═╝╚═╝
```

Structural variant toolkit for benchmarking, annotating and more for VCFs

[WIKI page](https://github.com/spiralgenetics/truvari/wiki) has detailed documentation.
See [Updates](https://github.com/spiralgenetics/truvari/wiki/Updates) on new versions.

## Installation
Truvari uses Python 3.7 and can be installed with pip:
```
  pip install Truvari 
```
[PyPi](https://pypi.org/project/Truvari/#history) has a history of all versions available. Pip installs all requirements EXCEPT external tools needed for running some annotations. See [anno](https://github.com/spiralgenetics/truvari/wiki/anno) for details. 

To build and install Truvari from scratch:
```
  python -m pip install --upgrade pip setuptools wheel
  python setup.py sdist bdist_wheel
  pip install dist/Truvari-<version>.tar.gz
```
Where `<version>` is which version you just built.

 See [tags/](https://github.com/spiralgenetics/truvari/tags/) for a list of all available versions.

## 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](https://github.com/spiralgenetics/truvari/wiki/bench) - Performance metrics from comparison of two VCFs
 - [stats](https://github.com/spiralgenetics/truvari/wiki/stats) - Basic SV relevant VCF stats
 - [consistency](https://github.com/spiralgenetics/truvari/wiki/consistency) - Consistency report between multiple VCFs
 - [anno](https://github.com/spiralgenetics/truvari/wiki/anno) - Add SV annotations to a VCF
 - [collapse](https://github.com/spiralgenetics/truvari/wiki/collapse) - Collapse possibly redundant VCF entries
 - [truv2df](https://github.com/spiralgenetics/truvari/wiki/truv2df) - Turn a Truvari directory's VCFs into a pandas DataFrame

## More Information

Find more details and discussions about Truvari on the [WIKI page](https://github.com/spiralgenetics/truvari/wiki).

[https://www.spiralgenetics.com](https://www.spiralgenetics.com)


