bedtools

bedtools is a powerful toolset for genome arithmetic.

Version:   v2.26.0
About:     developed in the quinlanlab.org and by many contributors worldwide.
Docs:      http://bedtools.readthedocs.io/
Code:      https://github.com/arq5x/bedtools2
Mail:      https://groups.google.com/forum/#!forum/bedtools-discuss

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.
    shift         Adjust the position of intervals.
    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.
    spacing       Report the gap lengths between intervals in a file.
    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.
    fisher        Calculate Fisher statistic b/w two feature 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.
    split         Split a file into multiple files with equal records or base pairs.

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