Sunday, April 1, 2012

Fwd: bedtools - (Version 2.16.2, 30-March-2012)

Bedtools has become as unmissable as Samtools for who works with NGS and it keeps improving (Thanks Aaron!). When added to Galaxy or other workflow bow, this should really be able of wonders (my 5 Euro-cents). I currently only use it at cli but see the potential for non-cli users.


below are the latest additions copied from the google code site:
Fwd: please follow footer link

* The -split command in intersectBed now applies to both the A and the B file.

* New tools: bedtools map, expand, random, makewindows, bamtofastq

* added -loj (left outer join) option to bedtools intersect. Behaves like a database left join and allows all A intervals to be reported. When overlaps exist, they are reported. When they don't, NULL B entries are reported for the A feature.

* Remote BAM files can now be read via HTTP or FTP. Support for remote BED/GFF/VCF will come in a future release.

* Added options to "bedtools closest" that ignore up- or down-stream intervals.

* Added count_distinct operation to groupby

* Added an initial version of a regression testing suite. invoke with "make test"

* When using -bed with BAM input in intersectBed, full BED12 features are produced

* Developed a standardized API for working with split BED and BAM intervals

* Support for "empty" columns: input files with consecutive delimiters are now supported

* Github commit number is now included in version number for easier tracking.

* Groupby now supports - for stdin

* New command line interface invoked with "bedtools command"


(Original Post: http://code.google.com/p/bedtools/.)