.. MIP_api documentation master file, created by
   sphinx-quickstart on Wed Sep  4 10:33:34 2013.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.


.. image:: _static/mip-logo.png

Release |version|.

`MIP <https://github.com/henrikstranneheim/MIP>`_ is a pipeline for clinical analysis of 
whole exome and whole genome sequence data.


Contents:

.. toctree::
   :maxdepth: 2
   
   MIP_overview
   change_log
   installation
   setup
   MIP_execution
   adding-new-programs
   structure
   vcfParser
   qcCollect
   rank_modelv1.18
   rank_modelv1.12
   rank_modelv1.11
   rank_modelv1.5
   svrank_modelv1.0
   configuration_file
   pedigree_file
   IDN
   the_code



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

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