Clara Parabricks Pipelines
===========================

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

   text/software_overview.rst
   text/getting_started.rst
   text/local_installation.rst

.. toctree::
   :maxdepth: 2
   :caption: Standalone Tools
   :name: Standalone Tools

   text/fastq_and_bam_processing.rst
   text/variant_callers.rst
   text/rna.rst
   text/qc_metrics.rst
   text/variant_processing.rst
   text/joint_calling.rst
   text/gvcf_processing.rst

.. toctree::
   :maxdepth: 2
   :caption: Pipelines
   :name: Pipelines

   text/germline_pipeline.rst
   text/deep_pipeline.rst
   text/human_par_pipeline.rst
   text/somatic_pipeline.rst
   text/rna_pipeline.rst

.. toctree::
   :maxdepth: 2
   :caption: FAQs and Troubleshooting
   :name: FAQs and Troubleshooting

   text/faq_and_troubleshooting.rst