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Commit 19a78963 authored by Aaron's avatar Aaron
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[DOC] update complement docs

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############### ###############
*complement* *complement*
############### ###############
**complementBed** returns the intervals in a genome that are not by the features in a feature file. An
example usage of this tool would be to return the intervals of the genome that are not annotated as a
repeat.
|
.. 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 and option summary
========================================================================== ==========================================================================
Usage: **Usage**:
:: ::
complementBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME>
**No additional options.** bedtools complement -i <BED/GFF/VCF> -g <GENOME>
**(or)**:
::
complementBed -i <BED/GFF/VCF> -g <GENOME>
========================================================================== ==========================================================================
Default behavior Default behavior
========================================================================== ==========================================================================
Figure: By default, ``bedtools complement`` returns all genomic intervals that are not
:: covered by at least one record from the input file.
Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BED FILE A ************* *************** ******************
Result === === ===== =======
.. code-block:: bash
For example: $ cat A.bed
::
cat A.bed
chr1 100 200 chr1 100 200
chr1 400 500 chr1 400 500
chr1 500 800 chr1 500 800
cat my.genome $ cat my.genome
chr1 1000 chr1 1000
chr2 800
$ bedtools complement -i A.bed -g my.genome
chr1 0 100
chr1 200 400
chr1 800 1000
chr2 0 800
complementBed -i A.bed -g my.genome
chr1 0 100
chr1 200 400
chr1 800 1000
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