████████╗██████╗ ██╗ ██╗██╗ ██╗ █████╗ ██████╗ ██╗
╚══██╔══╝██╔══██╗██║ ██║██║ ██║██╔══██╗██╔══██╗██║
██║ ██████╔╝██║ ██║██║ ██║███████║██████╔╝██║
██║ ██╔══██╗██║ ██║╚██╗ ██╔╝██╔══██║██╔══██╗██║
██║ ██║ ██║╚██████╔╝ ╚████╔╝ ██║ ██║██║ ██║██║
╚═╝ ╚═╝ ╚═╝ ╚═════╝ ╚═══╝ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝
Toolkit for benchmarking, merging, and annotating Structrual Variants
WIKI page has detailed documentation.
See Updates on new versions.
Read our Paper for more details.
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 -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
- divide - Divide a VCF into independent parts
- segment - Normalization of SVs into disjointed genomic regions
More Information
Find more details and discussions about Truvari on the WIKI page.
1 maintainer
Metadata
1 maintainer
Release files for truvari 3.5.0
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-3.5.0.tar.gz | 59.9 kB | Details |
Built distributions (wheels)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| Truvari-3.5.0-py3.9.egg | Legacy Egg format | - | - | Details |
| Truvari-3.5.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 318.3 kB
Release files / Truvari-3.5.0.tar.gz
| Download URL | Truvari-3.5.0.tar.gz |
|---|---|
| Size | 59.9 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
d3f0234c50b08b28a27484c3d18c26e5c2e9dae4ed56a48a5029458849c164d1
|
|
BLAKE2b-256 checksum How to use checksums |
04a5fa45625c9595b2f6e100984f770f17c5d2272790b0bb9d971c2c190c1cb4
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.9.13
|
Release files / Truvari-3.5.0-py3.9.egg
| Download URL | Truvari-3.5.0-py3.9.egg |
|---|---|
| Size | 179.7 kB |
| Tags | Egg |
|
SHA-256 checksum How to use checksums |
1b1ceb8c5696504806be60d304a5bf56f8e519e7e656d77557b11cf7272b68e4
|
|
BLAKE2b-256 checksum How to use checksums |
afddc48add7a8f5c8c46f8545277ee2a73bd3783ba69c5d39fdd28f5f06e0945
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.9.13
|
Release files / Truvari-3.5.0-py3-none-any.whl
| Download URL | Truvari-3.5.0-py3-none-any.whl |
|---|---|
| Size | 78.7 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
7cecced136bf99b6f6184bcf9bd384a79ecb4f5e0cc5a4ed09c6836b5be2b8ff
|
|
BLAKE2b-256 checksum How to use checksums |
0de4d3deacb1581c099cf834ea55cdf74314766657a1b1da7dfca1765c3d12cf
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.9.13
|
