Sunday, February 6, 2011

BEDTools (2.11.2 and keeps growing)

Version 2.11.2: "Hi all,
Version 2.11.2 has just been posted. I adds the 'max distance (-d)' functionality back to mergeBed. I reimplemented the mergeBed algorithm for the 2.11 release and neglected to add this logic. Apologies for the inconvenience.

= content (from readme file) ======
*intersectBed (BAM)*
Returns overlaps between two BED/GFF/VCF files.
*pairToBed (BAM)*
Returns overlaps between a paired-end BED file and a regular BED/VCF/GFF file.
*bamToBed (BAM)*
Converts BAM alignments to BED6, BED12, or BEDPE format.
*bedToBam (BAM)*
Converts BED/GFF/VCF features to BAM format.
Converts "blocked" BED12 features to discrete BED6 features.
Creates IGV batch scripts for taking multiple snapshots from BED/GFF/VCF features.
*coverageBed (BAM)*
Summarizes the depth and breadth of coverage of features in one BED versus features (e.g, "windows", exons, etc.) defined in another BED/GFF/VCF file.
*genomeCoverageBed (BAM)*
Creates either a histogram, BEDGRAPH, or a "per base" report of genome coverage.
Combines multiple BedGraph files into a single file, allowing coverage/other comparisons between them.
Annotates one BED/VCF/GFF file with overlaps from many others.
Summarizes data in a file/stream based on common columns.
Returns the number of bases pairs of overlap b/w two features on the same line.
*pairToPair *
Returns overlaps between two paired-end BED files.
Returns the closest feature to each entry in a BED/GFF/VCF file.
Removes the portion of an interval that is overlapped by another feature.
*windowBed (BAM)*
Returns overlaps between two BED/VCF/GFF files based on a user-defined window.
Merges overlapping features into a single feature.
Returns all intervals _not_ spanned by the features in a BED/GFF/VCF file.
Creates FASTA sequences based on intervals in a BED/GFF/VCF file.
Masks a FASTA file based on BED coordinates.
Randomly permutes the locations of a BED file among a genome.
Adjusts each BED entry by a requested number of base pairs.
Sorts a BED file by chrom, then start position. Other ways as well.
Creates an HTML file of links to the UCSC or a custom browser.

(Via BEDtools.)