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The BEDTools suite
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This section covers the functionality and default / optional usage for each of the available BEDTools.
Example "figures" are provided in some cases in an effort to convey the purpose of the tool. The
behavior of each available parameter is discussed for each tool in abstract terms. More concrete usage
examples are provided in **Section 6**.


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Table of contents
=================
.. toctree::
   :maxdepth: 1

   intersectBed
   pairToBed
   pairToPair
   bamToBed
   windowBed
   closestBed
   subtractBed
   mergeBed
   coverageBed
   genomecoverageBed
   fastafromBed
   maskfastafromBed
   shuffleBed
   slopBed
   sortBed
   linksBed
   complementBed
   bedToBam
   overlap
   bedToIgv
   bed12ToBed6
   groupBy
   unionBedGraphs
   annotateBed