$ bedtools multiinter -examples

Tool:    bedtools multiinter (aka multiIntersectBed)
Version: v2.19.1-213-ga1aa1ae-dirty
Summary: Identifies common intervals among multiple
     BED/GFF/VCF files.

Usage:   bedtools multiinter [OPTIONS] -i FILE1 FILE2 .. FILEn
     Requires that each interval file is sorted by chrom/start. 

Options: 
    -cluster    Invoke Ryan Layers's clustering algorithm.

    -header     Print a header line.
            (chrom/start/end + names of each file).

    -names      A list of names (one/file) to describe each file in -i.
            These names will be printed in the header line.

    -g      Use genome file to calculate empty regions.
            - STRING.

    -empty      Report empty regions (i.e., start/end intervals w/o
            values in all files).
            - Requires the '-g FILE' parameter.

    -filler TEXT    Use TEXT when representing intervals having no value.
            - Default is '0', but you can use 'N/A' or any text.

    -examples   Show detailed usage examples.

Example usage:

== Input files: ==

 $ cat a.bed
 chr1  6   12
 chr1  10  20
 chr1  22  27
 chr1  24  30

 $ cat b.bed
 chr1  12  32
 chr1  14  30

 $ cat c.bed
 chr1  8   15
 chr1  10  14
 chr1  32  34

 $ cat sizes.txt
 chr1  5000

== Multi-intersect the files: ==

 $ multiIntersectBed -i a.bed b.bed c.bed
chr1    6   8   1   1   1   0   0
chr1    8   12  2   1,3 1   0   1
chr1    12  15  3   1,2,3   1   1   1
chr1    15  20  2   1,2 1   1   0
chr1    20  22  1   2   0   1   0
chr1    22  30  2   1,2 1   1   0
chr1    30  32  1   2   0   1   0
chr1    32  34  1   3   0   0   1

== Multi-intersect the files, with a header line (titles are the file names): ==

 $ multiIntersectBed -header -i a.bed b.bed c.bed
 chrom  start   end num list    a.bed   b.bed   c.bed
 chr1   6   8   1   1   1   0   0
 chr1   8   12  2   1,3 1   0   1
 chr1   12  15  3   1,2,3   1   1   1
 chr1   15  20  2   1,2 1   1   0
 chr1   20  22  1   2   0   1   0
 chr1   22  30  2   1,2 1   1   0
 chr1   30  32  1   2   0   1   0
 chr1   32  34  1   3   0   0   1

== Multi-intersect the files, with a header line and custom names: ==

 $ multiIntersectBed -header -i a.bed b.bed c.bed -names A B C
 chrom  start   end num list    A   B   C
 chr1   6   8   1   A   1   0   0
 chr1   8   12  2   A,C 1   0   1
 chr1   12  15  3   A,B,C   1   1   1
 chr1   15  20  2   A,B 1   1   0
 chr1   20  22  1   B   0   1   0
 chr1   22  30  2   A,B 1   1   0
 chr1   30  32  1   B   0   1   0
 chr1   32  34  1   C   0   0   1

== Multi-intersect the files, showing empty regions (note, requires -g): ==

 $ multiIntersectBed -header -i a.bed b.bed c.bed -names A B C -empty -g sizes.txt
 chrom  start   end num list    A   B   C
 chr1   0   6   0   none    0   0   0
 chr1   6   8   1   A   1   0   0
 chr1   8   12  2   A,C 1   0   1
 chr1   12  15  3   A,B,C   1   1   1
 chr1   15  20  2   A,B 1   1   0
 chr1   20  22  1   B   0   1   0
 chr1   22  30  2   A,B 1   1   0
 chr1   30  32  1   B   0   1   0
 chr1   32  34  1   C   0   0   1
 chr1   34  5000    0   none    0   0   0