.. SMAP documentation master file, created by
   sphinx-quickstart on Wed Aug  5 13:28:17 2020.
   You can adapt this file completely to your liking, but it should at least
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.. _SMAPhaploindex:

SMAP haplotype-sites
====================

| This is the manual for the SMAP haplotype-sites component of the SMAP package. 
| The first step prior to running **SMAP haplotype-sites** is the definition of the locus start and end points. 
| For HiPlex and Shotgun data these can be created using Python scripts provided in the Utility tools.
| For GBS data, **SMAP delineate** should be run to define relevant loci and read mapping polymorphisms in a data-driven manner.
| The scheme below depicts the two major distinctions, concerning library preparation method and sample type, implemented in this program.

.. image:: ../images/sites/haplotype_step_scheme_1-6.png

.. toctree::
   :maxdepth: 2
   :caption: Contents:
   
   sites_scope_usage
   sites_feature_description/index
   sites_HIW.rst
   sites_examples
   sites_faq