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The BEDTools suite
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`bedtools` consists of a suite of sub-commands that are invoked as follows::

    bedtools [sub-command] [options]

For example, to intersect two BED files, one would invoke the following::

    bedtools intersect -a a.bed -b b.bed

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The full list of `bedtools` sub-commands.
=========================================
.. toctree::
   :maxdepth: 1

   tools/annotate   
   tools/bamtobed    
   tools/bamtofastq  
   tools/bed12tobed6 
   tools/bedpetobam  
   tools/bedtobam    
   tools/closest    
   tools/cluster    
   tools/complement 
   tools/coverage   
   tools/expand     
   tools/flank      
   tools/fisher
   tools/genomecov  
   tools/getfasta    
   tools/groupby    
   tools/igv        
   tools/intersect  
   tools/jaccard    
   tools/links      
   tools/makewindows
   tools/map        
   tools/maskfasta   
   tools/merge      
   tools/multicov    
   tools/multiinter  
   tools/nuc         
   tools/overlap    
   tools/pairtobed   
   tools/pairtopair  
   tools/random     
   tools/reldist    
   tools/shift      
   tools/shuffle    
   tools/slop       
   tools/sort       
   tools/subtract
   tools/summary   
   tools/tag         
   tools/unionbedg   
   tools/window