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Structural variant toolkit for benchmarking, annotating and more for VCFs
WIKI page has detailed documentation. See Updates on new versions.
Installation
Truvari uses Python 3.6+ and can be installed with pip:
python3 -m pip install Truvari
PyPi has a history of all versions available. Pip installs all requirements EXCEPT external tools needed for running some annotations. See anno for details.
To build and install Truvari from scratch:
python3 setup.py install
See tags/ for a list of all available versions.
See Development/docker for instructions on how to build and use a Truvari Docker container.
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 - Performance metrics from comparison of two VCFs
- collapse - Collapse possibly redundant VCF entries
- anno - Add SV annotations to a VCF
- vcf2df - Turn a VCF into a pandas DataFrame
- consistency - Consistency report between multiple VCFs
More Information
Find more details and discussions about Truvari on the WIKI page.
1 maintainer
Metadata
1 maintainer
Release files for truvari 3.0.1
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-3.0.1.tar.gz | 39.1 kB | Details |
Built distributions (wheels)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| Truvari-3.0.1-py3.9.egg | Legacy Egg format | - | - | Details |
| Truvari-3.0.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 210.5 kB
Release files / Truvari-3.0.1.tar.gz
| Download URL | Truvari-3.0.1.tar.gz |
|---|---|
| Size | 39.1 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.2 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.9.7
|
Release files / Truvari-3.0.1-py3.9.egg
| Download URL | Truvari-3.0.1-py3.9.egg |
|---|---|
| Size | 118.6 kB |
| Tags | Egg |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.2 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.9.7
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Release files / Truvari-3.0.1-py3-none-any.whl
| Download URL | Truvari-3.0.1-py3-none-any.whl |
|---|---|
| Size | 52.8 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.2 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.9.7
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