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Manipulate tabular genomic files.

SimilarTo.png: BEDOps

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The BEDTools [1] utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together.

The following are examples of common questions that one can address with BEDTools.

  • Intersecting two BED files in search of overlapping features.
  • Culling/refining/computing coverage for BAM alignments based on genome features.
  • Merging overlapping features.
  • Screening for paired-end (PE) overlaps between PE sequences and existing genomic features.
  • Calculating the depth and breadth of sequence coverage across defined "windows" in a genome.
  • Screening for overlaps between "split" alignments and genomic features.

The fact that all of the BEDTools accept input from “standard input (stdin)” allows one to “stream / pipe” several commands together to facilitate more complicated analyses. Also, the tools allow fine control over how output is reported. Most recently, I have added support for sequence alignments in BAM ( format, as well as for features in VCF and GFF, as well as “blocked” BED format. The tools are quite fast and typically finish in a matter of a few seconds, even for large datasets.

You can obtain bedtools as a zipped source folder or by using GIT (better) from the following repository [2].
A picture-rich operation manual is hosted at [3].

Technical.png Python Afficionados, can download a python version of BEDTools used in Galaxy

# bedtools_v2.19.1

$ bedtools
bedtools: flexible tools for genome arithmetic and DNA sequence analysis.
usage:    bedtools <subcommand> [options]

The bedtools sub-commands include:

[ Genome arithmetic ]
    intersect     Find overlapping intervals in various ways.
    window        Find overlapping intervals within a window around an interval.
    closest       Find the closest, potentially non-overlapping interval.
    coverage      Compute the coverage over defined intervals.
    map           Apply a function to a column for each overlapping interval.
    genomecov     Compute the coverage over an entire genome.
    merge         Combine overlapping/nearby intervals into a single interval.
    cluster       Cluster (but don't merge) overlapping/nearby intervals.
    complement    Extract intervals _not_ represented by an interval file.
    subtract      Remove intervals based on overlaps b/w two files.
    slop          Adjust the size of intervals.
    flank         Create new intervals from the flanks of existing intervals.
    sort          Order the intervals in a file.
    random        Generate random intervals in a genome.
    shuffle       Randomly redistrubute intervals in a genome.
    sample        Sample random records from file using reservoir sampling.
    annotate      Annotate coverage of features from multiple files.

[ Multi-way file comparisons ]
    multiinter    Identifies common intervals among multiple interval files.
    unionbedg     Combines coverage intervals from multiple BEDGRAPH files.

[ Paired-end manipulation ]
    pairtobed     Find pairs that overlap intervals in various ways.
    pairtopair    Find pairs that overlap other pairs in various ways.

[ Format conversion ]
    bamtobed      Convert BAM alignments to BED (& other) formats.
    bedtobam      Convert intervals to BAM records.
    bamtofastq    Convert BAM records to FASTQ records.
    bedpetobam    Convert BEDPE intervals to BAM records.
    bed12tobed6   Breaks BED12 intervals into discrete BED6 intervals.

[ Fasta manipulation ]
    getfasta      Use intervals to extract sequences from a FASTA file.
    maskfasta     Use intervals to mask sequences from a FASTA file.
    nuc           Profile the nucleotide content of intervals in a FASTA file.

[ BAM focused tools ]
    multicov      Counts coverage from multiple BAMs at specific intervals.
    tag           Tag BAM alignments based on overlaps with interval files.

[ Statistical relationships ]
    jaccard       Calculate the Jaccard statistic b/w two sets of intervals.
    reldist       Calculate the distribution of relative distances b/w two files.

[ Miscellaneous tools ]
    overlap       Computes the amount of overlap from two intervals.
    igv           Create an IGV snapshot batch script.
    links         Create a HTML page of links to UCSC locations.
    makewindows   Make interval "windows" across a genome.
    groupby       Group by common cols. & summarize oth. cols. (~ SQL "groupBy")
    expand        Replicate lines based on lists of values in columns.

[ General help ]
    --help        Print this help menu.
    --version     What version of bedtools are you using?.
    --contact     Feature requests, bugs, mailing lists, etc.

  1. Aaron R Quinlan, Ira M Hall
    BEDTools: a flexible suite of utilities for comparing genomic features.
    Bioinformatics: 2010, 26(6);841-2
    [PubMed:20110278] ##WORLDCAT## [DOI] (I p)


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