Toolkit for benchmarking, merging, and annotating Structrual Variants
📚 WIKI page has detailed documentation.
📈 See Updates on new versions.
📝 Read our Paper 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 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 -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
- 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
🔎 More Information
All documentation about Truvari is on the WIKI. Additional information about using Truvari can be found in Discussions
1 maintainer
Metadata
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Release files for truvari 4.0.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| Truvari-4.0.0.tar.gz | 69.0 kB | Details |
Built distributions (wheels)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| Truvari-4.0.0-py3.9.egg | Legacy Egg format | - | - | Details |
| Truvari-4.0.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 361.5 kB
Release files / Truvari-4.0.0.tar.gz
| Download URL | Truvari-4.0.0.tar.gz |
|---|---|
| Size | 69.0 kB |
| Tags | Source |
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No |
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Release files / Truvari-4.0.0-py3.9.egg
| Download URL | Truvari-4.0.0-py3.9.egg |
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| Size | 203.8 kB |
| Tags | Egg |
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No |
| Uploaded via |
twine/4.0.2 CPython/3.9.16
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Release files / Truvari-4.0.0-py3-none-any.whl
| Download URL | Truvari-4.0.0-py3-none-any.whl |
|---|---|
| Size | 88.8 kB |
| Tags | Python 3 |
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No |
| Uploaded via |
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