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).

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

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

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

1. Unpack the source downloaded tarball.
2. cd into the expanded folder.
3. Type "make clean" and hit enter.
4. 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

1. Copy the files in bin/ to ~/bin or if you have the privileges, to /usr/local/bin.
2. Use the tools.