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quinlana 04-22-2009 08:40 PM

BED Tools for genomic intervals
Hi all,
I recently completed a new suite of BED Tools for comparing, among other things, overlapping intervals of genomic features in UCSC BED format.

Much of the functionality is analogous to that available on Galaxy's website. While I find Galaxy to be sublime, I much prefer doing such analyses on the command line, especially for large datasets such as those created by next-gen platforms.

These tools allow one to answer questions such as:
Which SNPs are in genes?
How many Illumina reads align to repetitive elements?
Which Segmental duplications overlap with CNVs?
How many genes are within a 10kb window of each of my CNVs?
What is the depth of sequencing coverage in my genome of interest?
I want to merge overlapping features into a single interval.
What intervals in the genome do not contain a repeat?

They are available for 64-bit LINUX and Intel Macs at:

Contact me if you have trouble or have feature requests. As time permits, I am happy to add new tools. The ones currently available were designed mainly for my needs, so I am certain I've neglected some obviously useful ones.

Also, I plan to post the source code in the next few days, as it will be a much easier way of supporting all the various OS/Chip flavors. Plus, others can hack the code to suit their needs.

All the best,

ewilbanks 04-23-2009 03:48 PM

Wow, thanks for making these available! I've been writing really hack versions of scripts to do a lot of this... so happy to have something more reliable!

quinlana 04-23-2009 08:32 PM

Source code now available.
Hi all,
I posted the source code for those that were having trouble with the available binaries. Installation instructions are now on the site as well as in the README you will download. I've also included some usage examples beyond what is on the website.


quinlana 04-27-2009 09:36 AM

Version 1.2
Hi all,
Just a note to let you know that a new release of BEDTools is now available.

What's new?

1. closestBed. Return the feature in B that is closest to A. If multiple features in B overlap A, the one with the highest overlap is returned.
2. windowBed. Added the ability to define separate windows for upstream and downstream overlaps.
3. subtractBed. Remove the portion of A that is overlapped by features in B.
4. linksBed. Creates an HTML file of intervals in a BED file. Handy for quickly navigating to interesting regions.


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