bedtools

TLDR

Intersect two files regarding the sequences' strand and save the result to the specified file

$ bedtools intersect -a [path/to/file_1] -b [path/to/file_2] -s > [path/to/output_file]

Intersect two files with a left outer join, i.e. report each feature from {{file_1}} and NULL if no overlap with {{file_2}}

$ bedtools intersect -a [path/to/file_1] -b [path/to/file_2] -lof > [path/to/output_file]

Using more efficient algorithm to intersect two pre-sorted files

$ bedtools intersect -a [path/to/file_1] -b [path/to/file_2] -sorted > [path/to/output_file]

Group file {{path/to/file}} based on the first three and the fifth column and summarize the sixth column by summing it up

$ bedtools groupby -i [path/to/file] -c 1-3,5 -g 6 -o sum

Convert bam-formatted file to a bed-formatted one

$ bedtools bamtobed -i [path/to/file].bam > [path/to/file].bed

Find for all features in {{file_1}}.bed the closest one in {{file_2}}.bed and write their distance in an extra column (input files must be sorted)

$ bedtools closest -a [path/to/file_1].bed -b [path/to/file_2].bed -d

bedtools is a powerful toolset for genome arithmetic.

Version:   v2.30.0
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  [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 redistribute 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.
    summary       Statistical summary of intervals in a file.

[ General Parameters ]
     --cram-ref    Reference used by a CRAM input

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

bedtools

bedtools

TLDR

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