.. Psychcore NGS Germline Variant Pipeline documentation master file, created by
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========
Contents
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Welcome to Psychcore NGS Germline Variant Pipeline's documentation!

About
=====

The following NGS pipeline was developed by the UCSF Psychiatry Bioinformatics Core (PsychCore) team to call variants on large cohorts of human sequencing data. The current build is can run on either whole genome or whole exome/targeted sequencing data.  This build can also call variants based on either reference genome GRCh37 (hg19) or GRCh38 (hg39). Please note that this pipeline is still being developed.

.. toctree::
   :maxdepth: 2

   Pipeline Overview <overview>
   Getting Started <getting-started>
   Configuration <conf>
   Running the Pipeline and its Output <out>
   Contact Us <contact>



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Indices and tables
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* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`