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.. _shift:
###############
*shift*
###############
|
.. image:: ../images/tool-glyphs/shift-glyph.png
:width: 600pt
|
``bedtools shift`` will move each feature in a feature file by a
user-defined number of bases. While something like this could be done with an
``awk '{OFS="\t" print $1,$2+<shift>,$3+<shift>}'``,
``bedtools shift`` will restrict the resizing to the size of the chromosome
(i.e. no features before 0 or past the chromosome end).
.. note::
In order to prevent the extension of intervals beyond chromosome boundaries,
``bedtools shift`` requires a *genome* file defining the length of each
chromosome or contig.
.. seealso::
:doc:`../tools/slop`
==========================================================================
Usage and option summary
==========================================================================
**Usage**:
::
bedtools shift [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-s or (-m and -p)]
**(or):**
::
shiftBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-s or (-m and -p)]
=========================== ===============================================================================================================================================================================================================
Option Description
=========================== ===============================================================================================================================================================================================================
**-s** Shift the BED/GFF/VCF entry -s base pairs. *Integer* or *Float* (e.g. 0.1) if used with -pct
**-m** Shift entries on the - strand -m base pairs. *Integer* or *Float* (e.g. 0.1) if used with -pct
**-p** Shift entries on the + strand -p base pairs. *Integer* or *Float* (e.g. 0.1) if used with -pct
**-pct** Define -s, -m and -p as a fraction of the feature's length. E.g. if used on a 1000bp feature, -s 0.50, will shift the feature 500 bp \"upstream\". Default = false.
**-header** Print the header from the input file prior to results.
=========================== ===============================================================================================================================================================================================================
==========================================================================
Default behavior
==========================================================================
By default, ``bedtools shift`` will shift features a fixed number of bases. This shift can either be applied to all features (``-s``), or seperately to features on the plus (``-p``) and minus (``-m``) strands. Shifts can either be positive or negative.
.. code-block:: bash
$ cat A.bed
chr1 5 100 +
chr1 800 980 -
$ cat my.genome
chr1 1000
$ bedtools shift -i A.bed -g my.genome -s 5
chr1 10 105 +
chr1 805 985 -
$ bedtools shift -i A.bed -g my.genome -p 2 -m -3
chr1 7 102 +
chr1 797 977 -
However, if the requested number of bases exceeds the boundaries of the
chromosome, ``bedtools shift`` will "clip" the feature accordingly.
.. code-block:: bash
$ cat A.bed
chr1 5 100 +
chr1 800 980 +
$ cat my.genome
chr1 1000
$ bedtools shift -i A.bed -g my.genome -s 5000
chr1 999 1000 +
chr1 999 1000 +
==========================================================================
``-pct`` Shifting features by a given fraction
==========================================================================
``bedtools shift`` will optionally increase the size of a feature by a
user-specific fraction.
For example:
.. code-block:: bash
$ cat A.bed
chr1 100 200 a1 1 +
$ bedtools shift -i A.bed -g my.genome -s 0.5 -pct
chr1 150 250 a1 1 +
==========================================================================
``-header`` Print the header for the A file before reporting results.
==========================================================================
By default, if your A file has a header, it is ignored when reporting results.
This option will instead tell bedtools to first print the header for the
A file prior to reporting results.
|
