Package: cutevariant
CutevariantA standalone and free application to explore genetics variations from VCF filePublished inBioinformatics AdvancedDocumentation available oncutevariant.labsquare.orgCutevariant 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.InstallationWindowsStandalone binary are available for windows:Download cutevariant 32 bitDownload cutevariant 64 bitLinuxIf 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--versionreturns at least3.32.
If not, run:# Uninstall previous versions of sqlite3 (to avoid conflicts)sudoaptremovesqlite3# Download latest sqlite versionwgethttps://www.sqlite.org/2022/sqlite-autoconf-3380500.tar.gz# Extract ittar-xvfsqlite-autoconf-3380500.tar.gzcdsqlite-autoconf-3380500
./configure# Run make to buildmake# Run make install, this will put the shared object in /usr/local/libsudomakeinstall# 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 itsource~/.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 sourcePyPiCutevariant is avaible fromPypi:pip install cutevariant # install
python -m cutevariant   # runFrom sourcePython 3.7 or newer is required# Clone repositorygitclonehttps://github.com/labsquare/cutevariant.gitcdcutevariant# Create a virtual environementpython3-mvirtualenvvenvsourcevenv/bin/activate# Install cutevariant in local modepython-mpipinstall-e# Run cutevariant as modulepython-mcutevariant# or `make run`# Run testpython-mpytesttestsUsagesYou can follow this tutorial to familiarize yourself with cutevarant.https://github.com/labsquare/cutevariant/wiki/Usage-examplesThe VQL langage specification is available here :https://github.com/labsquare/cutevariant/wiki/VQL-languageContributions / BugsCutevariant is a new project and all contributors are welcomeIssuesIf you found a bug or have a feature request, you can report it from theGithub isse trackers.Create a pluginDocumentation to create a plugin isavailable hereChatYou can join uson discord. We are speaking french right now, but we can switch to english.LicensesThis 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, seehttps://www.gnu.org/licenses/gpl-3.0.txt.