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.. _subtract:
###############
*subtract*
###############
|
.. image:: ../images/tool-glyphs/subtract-glyph.png
:width: 600pt
|
``bedtools subtract`` searches for features in B that overlap A. If an
overlapping feature is found in B, the overlapping portion is removed from A
and the remaining portion of A is reported. If a feature in B overlaps all of a
feature in A, the A feature will not be reported.
===============================
Usage and option summary
===============================
**Usage**:
::
bedtools subtract [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
**(or)**:
::
subtractBed [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
=========================== ===============================================================================================================================================================================================================
Option Description
=========================== ===============================================================================================================================================================================================================
**-f** Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
**-F** Minimum overlap required as a fraction of B. Default is 1E-9 (i.e., 1bp).
**-r** Require that the fraction of overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.
**-e** Require that the minimum fraction be satisfied for A _OR_ B. In other words, if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied.**-s** Force "strandedness". That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand.
**-S** Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. By default, overlaps are reported without respect to strand.
**-A** Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or ``-f`` amount), the entire feature is removed.
**-N** Same as -A except when used with -f, the amount is the sum of all features (not any single feature).
=========================== ===============================================================================================================================================================================================================
==========================================================================
Default behavior
==========================================================================
By default, ``bedtools subtracts`` removes each overlapping interval in B
from A. If a feature in B *completely* overlaps a feature in A, the A feature
is removed.
.. code-block:: bash
$ cat A.bed
chr1 10 20
chr1 100 200
$ cat B.bed
chr1 0 30
chr1 180 300
$ bedtools subtract -a A.bed -b B.bed
chr1 100 180
==========================================================================
``-f`` Requiring a minimal overlap fraction before subtracting
==========================================================================
This option behaves the same as the ``-f`` option for ``bedtools intersect``.
In this case, ``subtract`` will only subtract an overlap with B if it covers at
least the fraction of A defined by ``-f``. If an overlap is found,
but it does not meet the overlap fraction, the original A feature is
reported without subtraction.
.. code-block:: bash
$ cat A.bed
chr1 100 200
$ cat B.bed
chr1 180 300
$ bedtools subtract -a A.bed -b B.bed -f 0.10
chr1 100 180
$ bedtools subtract -a A.bed -b B.bed -f 0.80
chr1 100 200
==========================================================================
``-s`` Enforcing same "strandedness"
==========================================================================
This option behaves the same as the ``-s`` option for ``bedtools intersect``
while scanning for features in B that should be subtracted from A.
.. code-block:: bash
$ cat A.bed
chr1 100 200 a1 1 +
$ cat B.bed
chr1 80 120 b1 1 +
chr1 180 300 b2 1 -
$ bedtools subtract -a A.bed -b B.bed -s
chr1 120 200 a1 1 +
==========================================================================
``-S`` Enforcing opposite "strandedness"
==========================================================================
This option behaves the same as the ``-s`` option for ``bedtools intersect``
while scanning for features in B that should be subtracted from A.
.. code-block:: bash
$ cat A.bed
chr1 100 200 a1 1 +
$ cat B.bed
chr1 80 120 b1 1 +
chr1 180 300 b2 1 -
$ bedtools subtract -a A.bed -b B.bed -S
chr1 100 180 a1 1 +
==========================================================================
``-A`` Remove features with any overlap
==========================================================================
Unlike the default behavior, the ``-A`` option will completely remove
a feature from A if it has even 1bp of overlap with a feature in B.
.. code-block:: bash
$ cat A.bed
chr1 100 200
$ cat B.bed
chr1 180 300
$ bedtools subtract -a A.bed -b B.bed
chr1 100 180
$ bedtools subtract -a A.bed -b B.bed -A
|
