.. SMAP documentation master file, created by
   sphinx-quickstart on Wed Aug 5 13:28:17 2020.
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.. _SMAPchromplotindex:

SMAP chromplot
==============

.. image:: ../images/logo/SMAP_logo_v3.png
   :width: 200px
   :align: right

| This is the manual for the **SMAP chromplot** module of the SMAP package.  

| **SMAP chromplot** is a module that visualizes the haplotypes relative to two specific reference samples :ref:`SMAP delineate <SMAPdelindex>`. 
| **SMAP chromplot** is a useful tool to identify heterozygosity, crossover events, the origin of introgressed segments, etc.
| **SMAP chromplot** can also be used to optimize bioinformatics parameter settings across all steps of read data analysis, including read `preprocessing <https://gbprocess.readthedocs.io/en/latest/gbs_data_processing.html>`_, read mapping (*e.g.* `BWA-MEM <http://bio-bwa.sourceforge.net/bwa.shtml>`_), and selection of high quality loci by :ref:`SMAP delineate <SMAPdelindex>`.

.. toctree::
   :maxdepth: 2
   :caption: Contents:
   
   chromplot_scope_usage
   chromplot_feature_description
   chromplot_HIW
   chromplot_examples