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Scope & Usage
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Scope
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:purple:`Comparisons across data sets, shared and unique loci`

**SMAP compare** analyzes the overlap (shared and unique loci) between two GBA data sets that have both been processed with :ref:`SMAP delineate <SMAPdelindex>`.
**SMAP compare** can be used to compare:

	1.	parameter settings during read `preprocessing <https://gbprocess.readthedocs.io/en/latest/gbs_data_processing.html>`_. 
	#.  parameter settings during read mapping (*e.g.* `BWA-MEM <http://bio-bwa.sourceforge.net/bwa.shtml>`_).
	#.  parameter settings during locus delineation (:ref:`SMAP delineate <SMAPdelindex>`).
	#.	sets of progeny derived from independent breeding lines to estimate transferability of marker sets across a breeding program.
	#.	a set of pools against their constituent individuals to estimate sensitivity of detection across the allele frequency spectrum (example shown below).
	#.	GBS experiments performed in different labs, to investigate if similar protocols lead to similar sets of loci, *i.e.* comparability of own data to external data.
	

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Integration in the SMAP workflow
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.. image:: ../images/compare/SMAP_global_scheme_home_compare.png

**SMAP compare** is run on BED files with locus positions, directly after **SMAP delineate**, **SMAP sliding-frames** or **SMAP design**, and before the BED files are used for **SMAP haplotype-sites**.  
**SMAP compare** works on GBS, HiPlex and Shotgun sequencing data.

Commands & options
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::

	smap compare <Set1.bed> <Set2.bed>