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

-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    -

-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

This tool is part of the bedtools package from the Quinlan laboratory.

Citation

If you use this tool in Galaxy, please cite:

Bjoern A. Gruening (2014), Galaxy wrapper