5.1.38. window

Similar to bedtools intersect, window searches for overlapping features in A and B. However, window adds a specified number (1000, by default) of base pairs upstream and downstream of each feature in A. In effect, this allows features in B that are “near” features in A to be detected.

5.1.38.1. Usage and option summary

Usage:

bedtools window [OPTIONS] [-a|-abam] -b <BED/GFF/VCF>

(or):

bedtools window [OPTIONS] [-a|-abam] -b <BED/GFF/VCF>

Option	Description
-abam	BAM file A. Each BAM alignment in A is compared to B in search of overlaps. Use “stdin” if passing A with a UNIX pipe: For example: samtools view -b <BAM> | bedtools window -abam stdin -b genes.bed
-ubam	Write uncompressed BAM output. The default is write compressed BAM output.
-bed	When using BAM input (-abam), write output as BED. The default is to write output in BAM when using -abam. For example: bedtools window -abam reads.bam -b genes.bed -bed
-w	Base pairs added upstream and downstream of each entry in A when searching for overlaps in B. Default is 1000 bp.
-l	Base pairs added upstream (left of) of each entry in A when searching for overlaps in B. Allows one to create assymetrical “windows”. Default is 1000bp.
-r	Base pairs added downstream (right of) of each entry in A when searching for overlaps in B. Allows one to create assymetrical “windows”. Default is 1000bp.
-sw	Define -l and -r based on strand. For example if used, -l 500 for a negative-stranded feature will add 500 bp downstream. By default, this is disabled.
-sm	Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand.
-Sm	Only report hits in B that overlap A on the opposite strand. By default, overlaps are reported without respect to strand.
-u	Write original A entry once if any overlaps found in B. In other words, just report the fact at least one overlap was found in B.
-c	For each entry in A, report the number of hits in B while restricting to -f. Reports 0 for A entries that have no overlap with B.
-v	Only report those entries in A that have no overlaps with B.
-header	Print the header from the A file prior to results.

5.1.38.2. Default behavior

By default, bedtools window adds 1000 bp upstream and downstream of each A feature and searches for features in B that overlap this “window”. If an overlap is found in B, both the original A feature and the original B feature are reported.

$ cat A.bed
chr1  100  200

$ cat B.bed
chr1  500  1000
chr1  1300 2000

$ bedtools window -a A.bed -b B.bed
chr1  100  200  chr1  500  1000

5.1.38.3. -w Defining a custom window size

Instead of using the default window size of 1000bp, one can define a custom, symmetric window around each feature in A using the -w option. One should specify the window size in base pairs. For example, a window of 5kb should be defined as -w 5000.

For example (note that in contrast to the default behavior, the second B entry is reported):

$ cat A.bed
chr1  100  200

$ cat B.bed
chr1  500  1000
chr1  1300 2000

$ bedtools window -a A.bed -b B.bed -w 5000
chr1  100  200  chr1  500   1000
chr1  100  200  chr1  1300  2000

5.1.38.4. -l and -r Defining assymteric windows

One can also define asymmetric windows where a differing number of bases are added upstream and downstream of each feature using the -l (upstream) and -r (downstream)** options.

Note

By default, the -l and -r options ignore strand. If you want to define upstream and downstream based on strand, use the -sw option (below) with the -l and -r options.

For example (note the difference between -l 200 and -l 300):

$ cat A.bed
chr1  1000  2000

$ cat B.bed
chr1  500   800
chr1  10000 20000

$ bedtools window -a A.bed -b B.bed -l 200 -r 20000
chr1  1000   2000  chr1  10000  20000

$ bedtools window -a A.bed -b B.bed -l 300 -r 20000
chr1  1000   2000  chr1  500    800
chr1  1000   2000  chr1  10000  20000

5.1.38.5. -sw Defining assymteric windows based on strand

Especially when dealing with gene annotations or RNA-seq experiments, you may want to define asymmetric windows based on “strand”. For example, you may want to screen for overlaps that occur within 5000 bp upstream of a gene (e.g. a promoter region) while screening only 1000 bp downstream of the gene. By enabling the -sw (“stranded” windows) option, the windows are added upstream or downstream according to strand. For example, imagine one specifies -l 5000, -r 1000 as well as the -sw option. In this case, forward stranded (“+”) features will screen 5000 bp to the left (that is, lower genomic coordinates) and 1000 bp to the right (that is, higher genomic coordinates). By contrast, reverse stranded (“-”) features will screen 5000 bp to the right (that is, higher genomic coordinates) and 1000 bp to the left (that is, lower genomic coordinates).

For example (note the difference between -l 200 and -l 300):

$ cat A.bed
chr1  10000  20000  A.forward  1  +
chr1  10000  20000  A.reverse  1  -

$ cat B.bed
chr1  1000   8000   B1
chr1  24000  32000  B2

$ bedtools window -a A.bed -b B.bed -l 5000 -r 1000 -sw
chr1  10000  20000  A.forward  1  +  chr1  1000   8000   B1
chr1  10000  20000  A.reverse  1  -  chr1  24000  32000  B2

5.1.38.6. -sm Enforcing matches with the same “strandedness”

This option behaves the same as the -s option for bedtools intersect while scanning for overlaps within the “window” surrounding A. That is, overlaps in B will only be included if the B interval is on the same strand as the A interval.

5.1.38.7. -Sm Enforcing matches with the opposite “strandedness”

This option behaves the same as the -S option for bedtools intersect while scanning for overlaps within the “window” surrounding A. That is, overlaps in B will only be included if the B interval is on the opposite strand as the A interval.

5.1.38.8. -u Reporting the presence/absence of at least one overlapping feature

This option behaves the same as for bedtools intersect. That is, even if multiple overlaps exist, each A interval will only be reported once.

5.1.38.9. -c Reporting the number of overlapping features

This option behaves the same as for bedtools intersect. That is, it will report the count of intervals in B that overlap each A interval.

5.1.38.10. -v Reporting the absence of any overlapping features

This option behaves the same as for bedtools intersect. That is, it will only report those intervals in A that have have zero overlaps in B.

5.1.38.11. -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.

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