cluster — bedtools 2.31.0 documentation

# cluster

Similar to 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).

See also

merge

## 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

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