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.
💻 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/
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
🧬 Truvari Commands
- 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
🔎 More Information
All documentation about Truvari is on the WIKI. Additional information about using Truvari can be found in Discussions
1 maintainer
Metadata
1 maintainer
Release files for truvari 4.3.1
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-4.3.1.tar.gz | 82.1 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| truvari-4.3.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 182.9 kB
Release files / truvari-4.3.1.tar.gz
| Download URL | truvari-4.3.1.tar.gz |
|---|---|
| Size | 82.1 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
aeb1bec08ad5fbd6a515c76806dfc4c3e67240fb89825049288f29935d49cf54
|
|
BLAKE2b-256 checksum How to use checksums |
6f83bf6837c2d07a3a9b7c522573b95d347eef12af01cc54e12ae7cd10eefd8d
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.9.19
|
Release files / truvari-4.3.1-py3-none-any.whl
| Download URL | truvari-4.3.1-py3-none-any.whl |
|---|---|
| Size | 100.8 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
c08a62fbc4fccc3df34eb01a56bb98380fba38411b02766b368465d99b7c46fd
|
|
BLAKE2b-256 checksum How to use checksums |
6035e11e591297225163274e400434945a460c1cc4d89eeab13d4125474c8138
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.9.19
|
