MCNV2 Toolbox
=============

Welcome to the MCNV2 documentation. MCNV2 is a technology-agnostic toolbox for CNV quality assessment using Mendelian Precision in parent–offspring trios.

.. note::
   
   This documentation covers both the interactive **Shiny application** and the **command-line interface (CLI)** for batch processing.

Getting Started
---------------

.. grid:: 2

   .. grid-item-card:: Installation
      :link: getting-started/installation
      :link-type: doc

      Install MCNV2 (R + Python) and validate your environment.

   .. grid-item-card:: Quickstart
      :link: getting-started/quickstart
      :link-type: doc

      Run your first Mendelian Precision analysis in minutes.

Tutorials
---------

.. grid:: 2

   .. grid-item-card:: Shiny Tutorial
      :link: tutorials/shiny_tutorial
      :link-type: doc

      Interactive exploration: filters, plots, exports.

   .. grid-item-card:: CLI Tutorial
      :link: tutorials/cli_tutorial
      :link-type: doc

      Batch runs, reproducible pipelines, and wrappers.

Core Concepts
-------------

- :doc:`user-guide/mendelian_precision` — Understand the MP metric
- :doc:`user-guide/inheritance` — Inheritance status calculation
- :doc:`user-guide/filtering` — Quality filters and their impact

.. toctree::
   :maxdepth: 1
   :caption: Getting Started
   :hidden:

   getting-started/index

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

   user-guide/index

.. toctree::
   :maxdepth: 1
   :caption: Tutorials
   :hidden:

   tutorials/index

.. toctree::
   :maxdepth: 1
   :caption: Reference
   :hidden:

   reference/index

.. toctree::
   :maxdepth: 1
   :caption: About
   :hidden:

   about/index

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

* :ref:`genindex`
* :ref:`search`