Structural variant comparison tool for VCFs
Project description
████████╗██████╗ ██╗ ██╗██╗ ██╗ █████╗ ██████╗ ██╗
╚══██╔══╝██╔══██╗██║ ██║██║ ██║██╔══██╗██╔══██╗██║
██║ ██████╔╝██║ ██║██║ ██║███████║██████╔╝██║
██║ ██╔══██╗██║ ██║╚██╗ ██╔╝██╔══██║██╔══██╗██║
██║ ██║ ██║╚██████╔╝ ╚████╔╝ ██║ ██║██║ ██║██║
╚═╝ ╚═╝ ╚═╝ ╚═════╝ ╚═══╝ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝
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
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
- segment - Normalization of SVs into disjointed genomic regions
More Information
Find more details and discussions about Truvari on the WIKI page.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Truvari-3.1.0.tar.gz
(44.8 kB
view hashes)
Built Distributions
Truvari-3.1.0-py3.9.egg
(130.7 kB
view hashes)
Truvari-3.1.0-py3-none-any.whl
(57.9 kB
view hashes)