.. marvel documentation master file.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to the MARVELous documentation
=====================================

MARVELous (Marion's Analysis of Rare Variant Effects in Large data) is a Python
toolkit for associating phenotypes with carriership of genetic variants.

The package performs variant extraction from genetic files (VCF, BGEN, PLINK)
and statistical association testing with various outcome types.

.. toctree::
   :maxdepth: 2
   :caption: Getting Started

   getting_started
   usage

.. toctree::
   :maxdepth: 2
   :caption: User Guide

   configuration
   tests_guide
   advanced

.. toctree::
   :maxdepth: 2
   :caption: Examples

   examples

.. toctree::
   :maxdepth: 2
   :caption: API

   api

.. toctree::
   :maxdepth: 2
   :caption: Project Admin

   contributing
   dev_guide_adding_config_options
   raising_issues


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`