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.
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Standalone binary are available for windows:
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
Cutevariant is avaible from Pypi :
pip install cutevariant # install
python -m cutevariant # run
- 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
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
Cutevariant is a new project and all contributors are welcome
If you found a bug or have a feature request, you can report it from the Github isse trackers.
Documentation to create a plugin is available here
You can join us on discord. We are speaking french right now, but we can switch to english.
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.