BEDTools
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
BEDTools is a collection of utilities for comparing, summarizing, and intersecting genomic features in BED, GTF/GFF, VCF and BAM formats.
Manual
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
Git
git clone git://github.com/arq5x/bedtools.git
Download tarball - that big gray button on the upper right.
- Unpack the source downloaded tarball.
- cd into the expanded folder.
- Type "make" and hit enter.
- 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
- Run the test suite with: "make test"
- 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
- Use the tools.