5.1.23. merge

bedtools merge combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features.

Note

bedtools merge 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

cluster complement

5.1.23.1. Usage and option summary

Usage:

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

(or):

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

Option	Description
-s	Force strandedness. That is, only merge features that are the same strand. By default, this is disabled.
-n	Report the number of BED entries that were merged. 1 is reported if no merging occurred.
-d	Maximum distance between features allowed for features to be merged. Default is 0. That is, overlapping and/or book-ended features are merged.
-nms	Report the names of the merged features separated by commas. Change delimiter with -delim
-scores	Report the scores of the merged features. Specify one of the following options for reporting scores: sum, min, max, mean, median, mode, antimode, collapse (i.e., print a semicolon-separated list)
-delim	Specify a custom delimiter for the -nms and -scores concat options Example: -delim "|" Default: ";"

5.1.23.2. Default behavior

By default, bedtools merge combines overlapping (by at least 1 bp) and/or bookended intervals into a single, “flattened” or “merged” interval.

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

$ bedtools merge -i A.bed
chr1  100  500
chr1  501  1000

5.1.23.3. -s Enforcing “strandedness”

The -s option will only merge 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 merge -i A.bed -s
chr1  100  250    +
chr1  501  1000   +
chr1  250  500    -

5.1.23.4. -n Reporting the number of features that were merged

The -n option will report the number of features that were combined from the original file in order to make the newly merged feature. If a feature in the original file was not merged with any other features, a “1” is reported.

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

$ bedtools merge -i A.bed -n
chr1  100  500  3
chr1  501  1000 1

5.1.23.5. -d Controlling how close two features must be in order to merge

By default, only overlapping or book-ended features are combined into a new feature. However, one can force merge 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 combined.

$ cat A.bed
chr1  100  200
chr1  501  1000

$ bedtools merge -i A.bed
chr1  100  200
chr1  501  1000

$ bedtools merge -i A.bed -d 1000
chr1  100  200  1000

5.1.23.6. -nms Reporting the names of the features that were merged

Occasionally, one might like to know that names of the features that were merged into a new feature. The -nms option will add an extra column to the merge output which lists (separated by semicolons) the names of the merged features.

$ cat A.bed
chr1  100  200  A1
chr1  150  300  A2
chr1  250  500  A3

$ bedtools merge -i A.bed -nms
chr1  100  500  A1,A2,A3

5.1.23.7. -scores Reporting the scores of the features that were merged

Similarly, we might like to know that scores of the features that were merged into a new feature. Enter the -scores option. One can specify how the scores from each overlapping interval should be reported.

$ cat A.bed
chr1  100  200  A1 1
chr1  150  300  A2 2
chr1  250  500  A3 3

$ bedtools merge -i A.bed -scores mean
chr1  100  500  2

$ bedtools merge -i A.bed -scores max
chr1  100  500  3

$ bedtools merge -i A.bed -scores collapse
chr1  100  500  1,2,3

5.1.23.8. -delim Change the delimiter for -nms and -scores collapse

One can override the use of a comma as the delimiter for the -nms and -scores collapse options via the use of the -delim option.

$ cat A.bed
chr1  100  200  A1
chr1  150  300  A2
chr1  250  500  A3

Compare:

$ bedtools merge -i A.bed -nms
chr1  100  500  A1,A2,A3

to:

$ bedtools merge -i A.bed -nms -delim "|"
chr1  100  500  A1|A2|A3

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