5.1.35. subtract¶
bedtools subtract 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.
5.1.35.1. Usage and option summary¶
Usage:
bedtools subtract [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
(or):
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, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand. |
| -S | Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. By default, overlaps are reported without respect to strand. |
| -A | Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or -f amount), the entire feature is removed. |
| -N | Same as -A except when used with -f, the amount is the sum of all features (not any single feature). |
5.1.35.2. Default behavior¶
By default, bedtools subtracts removes each overlapping interval in B from A. If a feature in B completely overlaps a feature in A, the A feature is removed.
$ cat A.bed
chr1 10 20
chr1 100 200
$ cat B.bed
chr1 0 30
chr1 180 300
$ bedtools subtract -a A.bed -b B.bed
chr1 100 180
5.1.35.3. -f Requiring a minimal overlap fraction before subtracting¶
This option behaves the same as the -f option for bedtools intersect. In this case, subtract 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.
$ cat A.bed
chr1 100 200
$ cat B.bed
chr1 180 300
$ bedtools subtract -a A.bed -b B.bed -f 0.10
chr1 100 180
$ bedtools subtract -a A.bed -b B.bed -f 0.80
chr1 100 200
5.1.35.4. -s Enforcing same “strandedness”¶
This option behaves the same as the -s option for bedtools intersect while scanning for features in B that should be subtracted from A.
$ cat A.bed
chr1 100 200 a1 1 +
$ cat B.bed
chr1 80 120 b1 1 +
chr1 180 300 b2 1 -
$ bedtools subtract -a A.bed -b B.bed -s
chr1 120 200 a1 1 +
5.1.35.5. -S Enforcing opposite “strandedness”¶
This option behaves the same as the -s option for bedtools intersect while scanning for features in B that should be subtracted from A.
$ cat A.bed
chr1 100 200 a1 1 +
$ cat B.bed
chr1 80 120 b1 1 +
chr1 180 300 b2 1 -
$ bedtools subtract -a A.bed -b B.bed -S
chr1 100 180 a1 1 +
5.1.35.6. -A Remove features with any overlap¶
Unlike the default behavior, the -A option will completely remove a feature from A if it has even 1bp of overlap with a feature in B.
$ cat A.bed
chr1 100 200
$ cat B.bed
chr1 180 300
$ bedtools subtract -a A.bed -b B.bed
chr1 100 180
$ bedtools subtract -a A.bed -b B.bed -A
