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Old 04-22-2009, 08:40 PM   #1
quinlana
Senior Member
 
Location: Charlottesville

Join Date: Sep 2008
Posts: 119
Default 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:
http://people.virginia.edu/~arq5x/bedtools.html

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,
Aaron

Last edited by quinlana; 04-23-2009 at 04:05 PM. Reason: typo; more info
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