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genomics variation viewer
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.vscode [core] add new banned chars and fixed vcf import from Montpellier Jul 13, 2019
cutevariant Back to development: 0.1.15 Jul 13, 2019
examples [tests] bedreader is now tested Jun 2, 2019
tests [core] bed support sub selection Jun 15, 2019
.appveyor.yml [appveyor] install schema .. @ysard, I am probably wrong somewhere May 23, 2019
.gitattributes [dev] Add .gitattributes for Python language May 5, 2019
.gitignore Untrack db files Mar 27, 2019
.prospector.yaml [dev] Update prospector commands and config file to track missing doc… May 5, 2019
.travis.yml [travis] don't know what's happen. requirements.txt file is missing May 19, 2019
LICENSE Initial commit Nov 2, 2018 add dark style May 22, 2019
Makefile [dev] Add directives and rules to build cx_freeze blob on Windaube May 18, 2019 update readme and fix #83 May 22, 2019
Untitled.ipynb change view method Dec 2, 2018 [gui] Columnquerywidget doesn't reload the whole tree when query changed Apr 21, 2019
icon.ico [win32] add application icon May 23, 2019
pytest.ini add test for Qt gui ! ( don't forget to update requirement ) Jan 4, 2019
setup.cfg allow future version of PySide2 Jun 15, 2019 packaging is complete. ready to be uploaded on pypi. Mar 1, 2019
umbrella.xmi [gui] Use pythonic setters/getters for query attribute; replace tabs … Apr 16, 2019


cutevariant is a light standalone viewer of genetic variation written in Python for Qt. It allows you to view and filter VCF and other format files.

Cutevariant example


pip install cutevariant # install
cutevariant             # run

Installation on Windows

Pyside2 is not currently (2019 May) functional on Cygwin, so Cutevariant will not work on Cygwin.

  • Install Python3.6+
  • Install like the previous chapter said.
  • Add the path of python scripts executables to your PATH variable; Something like:


Two executables are generated in this directory:

- cutevariant_win_dbg.exe: Open a console in background to see debugging messages.

Note: Qt libs seems to have a very high loglevel and such a verbosity could make the program unusable.

- cutevariant.exe: Standard executable.

Developement in progress

Complete rewriting from Cpp to Python.

To get tests running

git clone
cd cutevariant
virtualenv -p /usr/bin/python3 venv
source ven/bin/activate
make install_deps # install
make run     # start application
make test    # start tests

Development & release cycle

Use zest.releaser to handle the version and distribution through pypi.

pip install zest.releaser[recommended]

To yield a new release, use:


Development on Windows (good luck)

  • Install Python3.6+

  • Install git

  • Install make (optional)

    pip install wheel git clone git fetch git checkout dev # or devel make install # or pip install --user -e .[dev]

Executable files are located here:

  • Executable path: C:\Users<username>\AppData\Roaming\Python\Python37\Scripts\cutevariant.exe

Build standalone program/archive/blob[add synonyms here] on Windows using cx_freeze

Strongly discouraged: You will generate an archive of 350Mo just for a program of less than 900Ko (including 550Ko of fonts and icons).

Install cx_freeze:

pip install cx_freeze

Build a blob:

make build_windows_blob

Your blob is in ./build/ directory.

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