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.. _flank:
###############
*flank*
###############
|
.. image:: ../images/tool-glyphs/flank-glyph.png
:width: 600pt
|
``bedtools flank`` will create two new flanking intervals for each interval in
a BED/GFF/VCF file. Note that ``flank`` will restrict the created flanking
intervals to the size of the chromosome (i.e. no start < 0 and no end >
chromosome size).
.. note::
In order to prevent creating intervals that violate chromosome boundaries,
``bedtools flank`` requires a *genome* file defining the length of each
chromosome or contig.
.. seealso::
:doc:`../tools/slop`
==========================================================================
Usage and option summary
==========================================================================
**Usage**:
::
bedtools flank [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
**(or):**
::
flankBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
=========================== ===============================================================================================================================================================================================================
Option Description
=========================== ===============================================================================================================================================================================================================
**-b** Increase the BED/GFF/VCF entry by the same number base pairs in each direction. *Integer*.
**-l** The number of base pairs to subtract from the start coordinate. *Integer*.
**-r** The number of base pairs to add to the end coordinate. *Integer*.
**-s** Define -l and -r based on strand. For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the *end* coordinate.
**-pct** Define -l and -r as a fraction of the feature's length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp "upstream". Default = false.
=========================== ===============================================================================================================================================================================================================
==========================================================================
Default behavior
==========================================================================
By default, ``bedtools flank`` will either add a fixed number of bases in each
direction (``-b``) or an asymmetric number of bases in each direction
with ``-l`` and ``-r``.
.. code-block:: bash
$ cat A.bed
chr1 100 200
chr1 500 600
$ cat my.genome
chr1 1000
$ bedtools flank -i A.bed -g my.genome -b 5
chr1 95 100
chr1 200 205
chr1 495 500
chr1 600 605
$ bedtools flank -i A.bed -g my.genome -l 2 -r 3
chr1 98 100
chr1 200 203
chr1 498 500
chr1 600 603
However, if the requested number of bases exceeds the boundaries of the
chromosome, ``bedtools flank`` will "clip" the feature accordingly.
.. code-block:: bash
$ cat A.bed
chr1 100 200
chr1 500 600
$ cat my.genome
chr1 1000
$ bedtools flank -i A.bed -g my.genome -b 800
chr1 0 100
chr1 200 1000
chr1 0 500
chr1 600 1000
==========================================================================
``-pct`` Resizing features by a given fraction
==========================================================================
``bedtools flank`` will optionally create flanking intervals whose size is
user-specified fraction of the original interval.
For example:
.. code-block:: bash
$ cat A.bed
chr1 100 200
chr1 500 700
################################################################
# note the flanking intervals from the second record in A.bed
# are 20bp whereas the flanking intervals from the first record
# are only 10bp
################################################################
$ bedtools flank -i A.bed -g my.genome -b 0.1 -pct
chr1 90 100
chr1 200 210
chr1 480 500
chr1 700 720
|
