=========================================
Whole Genome and Whole Exome Sequencing Modules 
=========================================

.. rst-class:: html-toggle
FASTQC
=======
.. automodule:: omics_pipe.modules.fastqc
	:members:

.. rst-class:: html-toggle	
BWA-MEM
==========
.. automodule:: omics_pipe.modules.bwa
	:members: bwa_mem
	
.. rst-class:: html-toggle
PICARD Mark Duplicates
================
.. automodule:: omics_pipe.modules.picard_mark_duplicates
	:members:
	
.. rst-class:: html-toggle
GATK Preprocessing
==============

WES
-------
.. automodule:: omics_pipe.modules.GATK_preprocessing_WES
	:members:
	
WGS
------
.. automodule:: omics_pipe.modules.GATK_preprocessing_WGS
	:members:

.. rst-class:: html-toggle
GATK Variant Discovery
================
.. automodule:: omics_pipe.modules.GATK_variant_discovery
	:members:
	
.. rst-class:: html-toggle
GATK Variant Filtering
=================
.. automodule:: omics_pipe.modules.GATK_variant_filtering
	:members: