subtract¶
bedtools subtract bedtools` subtract searches for features in B that overlap A by at least the number of base pairs given by the -f option. 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. If a feature in B does not overlap a feature in A by at least the -f amount, the A feature will be reported in its entirety.
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). |
-F |
Minimum overlap required as a fraction of B. Default is 1E-9 (i.e., 1bp). |
-r |
Require that the fraction of overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B. |
-e |
Require that the minimum fraction be satisfied for A _OR_ B. In other words, if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied. |
-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 |
-N |
Same as -A except when used with -f, the amount is the sum of all features (not any single feature). |
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
-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
-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 +
-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 +
-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
