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.. _multiinter:
###############
*multiinter*
###############
|
.. image:: ../images/tool-glyphs/multiinter-glyph.png
:width: 600pt
|
``bedtools multiinter`` identifies common intervals among multiple (and subsets thereof)
sorted BED/GFF/VCF files.
.. note::
1. All files must be sorted in the same mmanner (e.g., ``sort -k 1,1 -k2,2n in.bed > in.sorted.bed``)
===============================
Usage and option summary
===============================
**Usage**:
::
bedtools multiinter [OPTIONS] -i FILE1 FILE2 .. FILEn
**(or)**:
::
multiIntersect [OPTIONS] -i FILE1 FILE2 .. FILEn
=========================== ===============================================================================================================================================================================================================
Option Description
=========================== ===============================================================================================================================================================================================================
**-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.
**-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 usage examples on the command line.
=========================== ===============================================================================================================================================================================================================
==========================================================================
Default behavior
==========================================================================
By default, ``bedtools multiinter`` will inspect all of the intervals in each input file and
report the sub-intervals that are overlapped by 0, 1, 2, ... N files.
The default output format is as follows:
1. chromosome (or entire genome)
2. 0-based start coordinate of the sub-interval.
3. 1-based end coordinate of the sub-interval.
4. The number of files whose intervals overlap this sub interval at least once.
5. The list of file numbers (by order on the command line) whose intervals overlap this sub interval at least once.
6. Columns reflecting whether each file had (1) or did not have (0) 1 or more intervals overlapping this sub interval.
For example:
.. code-block:: bash
$ 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
$ bedtools multiinter -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
==========================================================================
``-header`` Add a header with columns names
==========================================================================
For example:
.. code-block:: bash
$ bedtools multiinter -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
==========================================================================
``-names`` Add custom labels for each file in the header
==========================================================================
For example:
.. code-block:: bash
$ bedtools multiinter -header -names A B C -i a.bed b.bed c.bed
chrom start end num list A B C
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
==========================================================================
``-empty`` Report the sub intervals not covered by any file
==========================================================================
Note that this option requires a ``-g`` file so that it knows the full
range of each chromosome or contig.
For example:
.. code-block:: bash
$ bedtools multiinter -header -names A B C -i a.bed b.bed c.bed -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
|
