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BEDTools
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Created by Aaron Quinlan Spring 2009.

Copyright 2009,2010,2011 Aaron Quinlan. All rights reserved.

Stable releases: http://code.google.com/p/bedtools

Repository: https://github.com/arq5x/bedtools

Released under GNU public license version 2 (GPL v2).

Summary
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BEDTools is a collection of utilities for comparing, summarizing, and
intersecting genomic features in BED, GTF/GFF, VCF and BAM formats.

Manual
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See the extensive PDF manual included at: http://code.google.com/p/bedtools/downloads/detail?name=BEDTools-User-Manual.v4.pdf.

This manual covers many common usage examples. There are also examples available at:
http://code.google.com/p/bedtools/wiki/Usage
http://code.google.com/p/bedtools/wiki/UsageAdvanced

Installation
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Git
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git clone git://github.com/arq5x/bedtools.git

Download tarball - that big gray button on the upper right.
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#. Unpack the source downloaded tarball.
#. cd into the expanded folder.
#. Type "make clean" and hit enter.
#. Type "make all" and hit enter.
#. If you encountered no errors, then all of the BED Tools should now be in bin/
If not, try to troubleshoot then email me: aaronquinlan at gmail dot com
#. Copy the files in bin/ to ~/bin or if you have the privileges, to /usr/local/bin.
#. Use the tools.