Friday, September 2, 2011

bedtools (Version 2.13.0, 1-Sept-2011)

BEDTools Latest news (shortened from the original page)


* New multiBamCov tool counts sequence coverage for multiple position-sorted bams at specific loci defined in a BED/GFF/VCF file
* New tabBam tool for annotating a BAM file with custom tag fields based on overlaps with BED/GFF/VCF files.

* New nuclBed tool profiles the nucleotide content of intervals in a fasta file.

* Support for FIFOs.

* New -counts option for coverageBed.

* New -S option for detecting overlaps on the opposite strand.

* Support for zero length features (i.e., start = end) such as insertions in the reference genome.

* slopBed can now extend the size of features by a percentage of it's size (-pct) instead of just a fixed number of bases.

* Two improvements to shuffleBed

* Native, "mix and match" support for BED, GFF, VCF (v4.0), BAM, and BEDPE files. All input files can be "gzipped"; such files are auto-detected.

* Proper support for "split" BAM alignments and "blocked" BED (aka BED12) features.

Citation
Please cite the following article if you use BEDTools in your research:

Quinlan, AR and Hall, IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.


This can be called a major list of improvements!
Also read http://obx.cphg.virginia.edu/quinlan/?p=368#comment-36 for nice examples and discussions.

(Via bedtools Google Code page.)