Cutevariant

A standalone and free application to explore genetics variations from VCF file

Published in Bioinformatics Advanced
Documentation available on cutevariant.labsquare.org

Cutevariant is a cross-plateform application dedicated to maniupulate and filter variation from annotated VCF file. When you create a project, data are imported into an sqlite database that cutevariant queries according your needs. Presently, SnpEff and VEP annotations are supported. Once your project is created, you can query variant using different gui controller or directly using the VQL language. This Domain Specific Language is specially designed for cutevariant and try to keep the same syntax than SQL for an easy use.

Installation

Windows

Standalone binary are available for windows:

• Download cutevariant 32 bit
• Download cutevariant 64 bit

Linux

If you run Linux, then you can either use PyPI or install from source. But before you proceed to installation, make sure that running this command:

sqlite3 --version

returns at least 3.32. If not, run:

# Uninstall previous versions of sqlite3 (to avoid conflicts)
sudo apt remove sqlite3
# Download latest sqlite version
wget https://www.sqlite.org/2022/sqlite-autoconf-3380500.tar.gz
# Extract it
tar -xvf sqlite-autoconf-3380500.tar.gz
cd sqlite-autoconf-3380500
./configure
# Run make to build
make
# Run make install, this will put the shared object in /usr/local/lib
sudo make install
# Then add LD_LIBRARY_PATH to your bash profile (either ~/.zshrc, ~/.bashrc, or whatever is your favorite)
echo "export LD_LIBRARY_PATH=/usr/local/lib" >> ~/.zshrc
# Source your shell profile so you don't have to restart it
source ~/.zshrc
#Now just to be sure:
sqlite3 --version
# You should see 3.38 now. If not, this means that the installation went wrong.
# That's it! Now you can install cutevariant, either from PyPI or directly from source

PyPi

Cutevariant is avaible from Pypi :

pip install cutevariant # install
python -m cutevariant   # run

From source

• Python 3.7 or newer is required

# Clone repository
git clone https://github.com/labsquare/cutevariant.git
cd cutevariant
# Create a virtual environement
python3 -m virtualenv venv 
source venv/bin/activate
# Install cutevariant in local mode
python -m pip install -e 
# Run cutevariant as module 
python -m cutevariant # or `make run`
# Run test 
python -m pytest tests

Usages

You can follow this tutorial to familiarize yourself with cutevarant.
https://github.com/labsquare/cutevariant/wiki/Usage-examples

The VQL langage specification is available here :
https://github.com/labsquare/cutevariant/wiki/VQL-language

Contributions / Bugs

Cutevariant is a new project and all contributors are welcome

Issues

If you found a bug or have a feature request, you can report it from the Github isse trackers.

Create a plugin

Documentation to create a plugin is available here

Chat

You can join us on discord. We are speaking french right now, but we can switch to english.

Licenses

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/gpl-3.0.txt.