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.. _complement:
###############
*complement*
###############
|
.. image:: ../images/tool-glyphs/complement-glyph.png
:width: 600pt
|
``bedtools complement`` returns all intervals in a genome that are **not**
covered by at least one interval in the input BED/GFF/VCF file.
.. seealso::
:doc:`../tools/merge`
==========================================================================
Usage and option summary
==========================================================================
**Usage**:
::
bedtools complement -i <BED/GFF/VCF> -g <GENOME>
**(or)**:
::
complementBed -i <BED/GFF/VCF> -g <GENOME>
==========================================================================
Default behavior
==========================================================================
By default, ``bedtools complement`` returns all genomic intervals that are not
covered by at least one record from the input file.
.. code-block:: bash
$ cat A.bed
chr1 100 200
chr1 400 500
chr1 500 800
$ cat my.genome
chr1 1000
chr2 800
$ bedtools complement -i A.bed -g my.genome
chr1 0 100
chr1 200 400
chr1 800 1000
chr2 0 800
==========================================================================
``-L`` Only report chromosomes that are in the `-i` file
==========================================================================
Use the "**-L**" option to `L`imit the output to solely the chromosomes
that are represented in the `-i` file. Chromosomes that are in `-g` but
not `-i` will be suppressed
For example (note the difference in coverage with and without **-s**:
.. code-block:: bash
$ cat A.bed
chr1 100 200
chr1 400 500
chr1 500 800
$ cat my.genome
chr1 1000
chr2 800
$ bedtools complement -i A.bed -g my.genome
chr1 0 100
chr1 200 400
chr1 800 1000
|
