truvari

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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 3.7 and can be installed with pip:

  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:

  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/ 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 - Performance metrics from comparison of two VCFs
stats - Basic SV relevant VCF stats
consistency - Consistency report between multiple VCFs
anno - Add SV annotations to a VCF
collapse - Collapse possibly redundant VCF entries
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://www.spiralgenetics.com

Metadata

Release files for truvari 2.1.1

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for truvari 2.1.1
File	Size	Uploaded
Truvari-2.1.1.tar.gz	43.2 kB	Mar 24, 2021	Details

Built distribution (wheel)

Table of built distributions (wheels) for truvari 2.1.1
File	Interpreter	ABI	Platform	Reset
Truvari-2.1.1-py3-none-any.whl 59.6 kB Mar 24, 2021	Python 3	none	any	Details

Total release size: 102.8 kB

Release files / Truvari-2.1.1.tar.gz

Download URL	Truvari-2.1.1.tar.gz
Size	43.2 kB
Tags	Source
SHA-256 checksum How to use checksums	`d770651e3b2bfe5dc796178491d69ecaa4ae02252d625de761c2e98457d53d2b`
BLAKE2b-256 checksum How to use checksums	`bd430cab0cb5343600cd9b342a0b2dc53ce6d6c18eee61ed42f5d9b085cfe196`
Upload date	Mar 24, 2021
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/3.3.0 pkginfo/1.7.0 requests/2.25.1 setuptools/50.3.2 requests-toolbelt/0.9.1 tqdm/4.56.0 CPython/3.6.9`

Release files / Truvari-2.1.1-py3-none-any.whl

Download URL	Truvari-2.1.1-py3-none-any.whl
Size	59.6 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`5f9b9dea1ea0b107d5306af43d76f56f1850231471dd6470fddd6bf9eadf8e6d`
BLAKE2b-256 checksum How to use checksums	`ef00a9f17f4a4cf8d0c064a759c904cfd6ba60a166bf909a3efdb50002ad6f74`
Upload date	Mar 24, 2021
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/3.3.0 pkginfo/1.7.0 requests/2.25.1 setuptools/50.3.2 requests-toolbelt/0.9.1 tqdm/4.56.0 CPython/3.6.9`