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.. _annotate:
###############
*annotate*
###############
``bedtools annotate``, well, annotates one BED/VCF/GFF file with the coverage
and number of overlaps observed from multiple other BED/VCF/GFF files.
In this way, it allows one to ask to what degree one feature coincides with
multiple other feature types with a single command.
==========================================================================
Usage and option summary
==========================================================================
**Usage**:
::
bedtools annotate [OPTIONS] -i <BED/GFF/VCF> -files FILE1 FILE2 FILE3 ... FILEn
**(or)**:
::
annotateBed [OPTIONS] -i <BED/GFF/VCF> -files FILE1 FILE2 FILE3 ... FILEn
=========================== ===============================================================================================================================================================================================================
Option Description
=========================== ===============================================================================================================================================================================================================
**-names** A list of names (one per file) to describe each file in -i. These names will be printed as a header line.
**-counts** Report the count of features in each file that overlap -i. Default behavior is to report the fraction of -i covered by each file.
**-both** Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of -i covered by each file.
**-s** Force strandedness. That is, only include hits in A that overlap B on the same strand. By default, hits are included 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.
=========================== ===============================================================================================================================================================================================================
==========================================================================
Default behavior - annotate one file with coverage from others.
==========================================================================
By default, the fraction of each feature covered by each annotation file is
reported after the complete feature in the file to be annotated.
.. code-block:: bash
$ cat variants.bed
chr1 100 200 nasty 1 -
chr2 500 1000 ugly 2 +
chr3 1000 5000 big 3 -
$ cat genes.bed
chr1 150 200 geneA 1 +
chr1 175 250 geneB 2 +
chr3 0 10000 geneC 3 -
$ cat conserve.bed
chr1 0 10000 cons1 1 +
chr2 700 10000 cons2 2 -
chr3 4000 10000 cons3 3 +
$ cat known_var.bed
chr1 0 120 known1 -
chr1 150 160 known2 -
chr2 0 10000 known3 +
$ bedtools annotate -i variants.bed -files genes.bed conserve.bed known_var.bed
chr1 100 200 nasty 1 - 0.500000 1.000000 0.300000
chr2 500 1000 ugly 2 + 0.000000 0.600000 1.000000
chr3 1000 5000 big 3 - 1.000000 0.250000 0.000000
==========================================================================
``-count`` Report the count of hits from the annotation files
==========================================================================
.. code-block:: bash
$ bedtools annotate -counts -i variants.bed -files genes.bed conserve.bed known_var.bed
chr1 100 200 nasty 1 - 2 1 2
chr2 500 1000 ugly 2 + 0 1 1
chr3 1000 5000 big 3 - 1 1 0
===========================================================================================
``-both`` Report both the count of hits and the fraction covered from the annotation files
===========================================================================================
.. code-block:: bash
$ bedtools annotate -both -i variants.bed -files genes.bed conserve.bed known_var.bed
#chr start end name score +/- cnt1 pct1 cnt2 pct2 cnt3 pct3
chr1 100 200 nasty 1 - 2 0.500000 1 1.000000 2 0.300000
chr2 500 1000 ugly 2 + 0 0.000000 1 0.600000 1 1.000000
chr3 1000 5000 big 3 - 1 1.000000 1 0.250000 0 0.000000
==========================================================================
``-s`` Restrict the reporting to overlaps on the **same** strand.
==========================================================================
.. code-block:: bash
$ bedtools annotate -s -i variants.bed -files genes.bed conserve.bed known_var.bed
chr1 100 200 nasty 1 - 0.000000 0.000000 0.000000
chr2 500 1000 ugly 2 + 0.000000 0.000000 0.000000
chr3 1000 5000 big 3 - 1.000000 0.000000 0.000000
==========================================================================
``-S`` Restrict the reporting to overlaps on the **opposite** strand.
==========================================================================
.. code-block:: bash
$ bedtools annotate -S -i variants.bed -files genes.bed conserve.bed known_var.bed
chr1 100 200 nasty 1 - 0.500000 1.000000 0.300000
chr2 500 1000 ugly 2 + 0.000000 0.600000 1.000000
chr3 1000 5000 big 3 - 0.000000 0.250000 0.000000
|
