5.7 subtractBed

subtractBed searches for features in B that overlap A. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported.

5.7.1 Usage and option summary

Usage:

subtractBed [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>

Option	Description
-f	Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
-s	Force strandedness. That is, find the closest feature in B overlaps A on the same strand. By default, this is disabled.

5.7.2 Default behavior

Figure:

Chromosome  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BED FILE A             *************            ******

BED File B         ^^^^^^^^                   ^^^^^^^^^^^

Result                     =========

For example:

cat A.bed
chr1  100  200
chr1  10   20

cat B.bed
chr1  0    30
chr1  180  300

subtractBed -a A.bed -b B.bed
chr1  100  180

5.7.3 (-f)Requiring a minimal overlap fraction before subtracting

This option behaves the same as the -f option for intersectBed. In this case, subtractBed will only subtract an overlap with B if it covers at least the fraction of A defined by -f. If an overlap is found, but it does not meet the overlap fraction, the original A feature is reported without subtraction.

For example:

cat A.bed
chr1  100  200

cat B.bed
chr1  180  300

subtractBed -a A.bed -b B.bed -f 0.10
chr1  100  180

subtractBed -a A.bed -b B.bed -f 0.80
chr1  100  200

5.7.4 (-s)Enforcing “strandedness”

This option behaves the same as the -s option for intersectBed while scanning for features in B that should be subtracted from A. See the discussion in the intersectBed section for details.