Tuesday, May 11, 2010

BEDtools - (Version 2.7.1, 6-May-2010)

previous posts on BEDtools:
  • bedtools - updated version 2.6.1 /
  • BEDTools: A flexible suite of utilities for comparing genomic features

    Latest news
    "Gzipped" BED, BEDPE and GFF files are now supported as input by all BEDTools. Such files must end in ".gz".
    New tool: bedToBam. Works with blocked and unblocked BED files. Useful for visualizing large BAM files (e.g. dbSNP) in IGV, Gambit, Tablet, etc.
    BAM support. intersectBed, pairToBed, coverageBed, windowBed, and genomeCoverageBed support alignment files in BAM format. Alignment end coordinates are now properly computed based on the CIGAR.
    Added an option (-wo) that reports the number of overlapping bases for each intersection b/w A and B files.
    Added an option (-wao) that reports the number of overlapping bases for each intersection b/w A and B files as well as 0 overlap for all features in A that do not overlap a feature in B.
    can now report coverage in BEDGRAPH format (-bg)
    can now report coverage in BEDGRAPH format (-bga) when coverage is zero for a given region.

    Table of supported utilities
    (BAM) denotes tools that support BAM alignment files.

    Utility Description
    intersectBed (BAM) Returns overlaps between two BED files.
    pairToBed (BAM) Returns overlaps between a paired-end BED file and a regular BED file.
    bamToBed (BAM) Converts BAM alignments to BED6, BED12, or BEDPE format.
    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 file.
    genomeCoverageBed (BAM) Creates either a histogram, BEDGRAPH, or a "per base" report of genome coverage.
    pairToPair Returns overlaps between two paired-end BED files.
    closestBed Returns the closest feature to each entry in a BED file.
    subtractBed Removes the portion of an interval that is overlapped by another feature.
    windowBed Returns overlaps between two BED files based on a user-defined window.
    mergeBed Merges overlapping features into a single feature.
    complementBed Returns all intervals not spanned by the features in a BED file.
    fastaFromBed Creates FASTA sequences based on intervals in a BED file.
    maskFastaFromBed Masks a FASTA file based on BED coordinates.
    shuffleBed Randomly permutes the locations of a BED file among a genome.
    slopBed Adjusts each BED entry by a requested number of base pairs.
    sortBed Sorts a BED file by chrom, then start position. Other ways as well.
    linksBed Creates an HTML file of links to the UCSC or a custom browser.

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