Thursday, April 8, 2010

bedtools - updated version 2.6.1 / Project Hosting on Google Code

Latest news (Version 2.6.1, 29-Mar-2010)

BAM support. intersectBed, pairToBed, coverageBed and genomeCoverageBed support alignment files in BAM format.

intersectBed: Added an option (-wo) that reports the number of overlapping bases for each intersection b/w A and B files.

coverageBed: can now report a histogram (-hist) of coverage for each feature in B. Useful for exome sequencing projects, for example. Runs faster

genomeCoverageBed: can now report coverage in BEDGRAPH format (-bg)

bamToBed: support for "blocked" BED (aka BED12) format (use the -bed12 option). This facilitates the creation of BED entries for "split" alignments (e.g. RNAseq or SV). When using BED12, one can specify an R,G,B color for the output for subsequent uploads to UCSC, Gambit, IGV, Tablet, etc.

fastaFromBed: added the ability to extract sequences from a FASTA file according to the strand in the BED file. That is, when "-" the extracted sequence is reverse complemented.

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