Command-line List
=================

These are the commands provided as part of NGS-Pipelilne.

General commands
----------------

.. toctree::
   :maxdepth: 1

   ngs-pl


Directory preparation commands
------------------------------

.. toctree::
   :maxdepth: 1

   generate-links


Execution commands
------------------

.. toctree::
   :maxdepth: 1

   run-targeted-variant-caller