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" and hit enter.
4. If you encountered no errors, then bedtools should now be in bin/

If not, try to troubleshoot then email me: aaronquinlan at gmail dot com

5. Run the test suite with: "make test"
6. Copy the files in bin/ to ~/bin or if you have the privileges, to /usr/local/bin. Make sure that the directory to which you copy the tools is in your $PATH
7. Use the tools.