5.24 annotateBed

annotateBed 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.

5.24.1 Usage and option summary

Usage:

annotateBed [OPTIONS] -i <BED/GFF/VCF> -files FILE1 FILE2 FILE3 ... FILEn

Option	Description
-namesr	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.

5.24.2 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.

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   +

annotateBed -i variants.bed -files genes.bed conserv.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

5.24.3 Report the count of hits from the annotation files

Figure:

annotateBed -counts -i variants.bed -files genes.bed conserv.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

5.24.4 Report both the count of hits and the fraction covered from the annotation files

Figure:

annotateBed -both -i variants.bed -files genes.bed conserv.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

5.24.5 Restrict the reporting to overlaps on the same strand.

Note: Compare with the result from 5.24.3

annotateBed -s -i variants.bed -files genes.bed conserv.bed known_var.bed
chr1  100   200   nasty  var1  -  0.000000  0.000000  0.000000
chr2  500   1000  ugly   var2  +  0.000000  0.000000  0.000000
chr3  1000  5000  big    var3  -  1.000000  0.000000  0.000000