cluster.rst

cluster

Similar to :doc:`../tools/merge`, cluster report each set of overlapping or "book-ended" features in an interval file. In contrast to merge, cluster does not flatten the cluster of intervals into a new meta-interval; instead, it assigns an unique cluster ID to each record in each cluster. This is useful for having fine control over how sets of overlapping intervals in a single interval file are combined.

Note

bedtools cluster requires that you presort your data by chromosome and then by start position (e.g., sort k1,1 -k2,2n in.bed > in.sorted.bed for BED files).

Usage and option summary

Usage:

bedtools cluster [OPTIONS] -i <BED/GFF/VCF>

(or):

clusterBed [OPTIONS] -i <BED/GFF/VCF>

Option	Description
-s	Force strandedness. That is, only cluster features that are the same strand. By default, this is disabled.
-d	Maximum distance between features allowed for features to be clustered. Default is 0. That is, overlapping and/or book-ended features are clustered.

Default behavior

By default, bedtools cluster collects overlapping (by at least 1 bp) and/or bookended intervals into distinct clusters. In the example below, the 4th column is the cluster ID.

$ cat A.bed
chr1  100  200
chr1  180  250
chr1  250  500
chr1  501  1000

$ bedtools cluster -i A.bed
chr1  100     200     1
chr1  180     250     1
chr1  250     500     1
chr1  501     1000    2

-s Enforcing "strandedness"

The -s option will only cluster intervals that are overlapping/bookended and are on the same strand.

$ cat A.bed
chr1  100  200   a1  1 +
chr1  180  250   a2  2 +
chr1  250  500   a3  3 -
chr1  501  1000  a4  4 +

$ bedtools cluster -i A.bed -s
chr1  100     200     a1      1       +       1
chr1  180     250     a2      2       +       1
chr1  501     1000    a4      4       +       2
chr1  250     500     a3      3       -       3

-d Controlling how close two features must be in order to cluster

By default, only overlapping or book-ended features are combined into a new feature. However, one can force cluster to combine more distant features with the -d option. For example, were one to set -d to 1000, any features that overlap or are within 1000 base pairs of one another will be clustered.

$ cat A.bed
chr1  100  200
chr1  501  1000

$ bedtools cluster -i A.bed
chr1  100  200    1
chr1  501  1000   2

$ bedtools cluster -i A.bed -d 1000
chr1  100  200    1
chr1  501  1000   1