subtract

Description

Remove intervals in A that overlap with B. Can either trim overlapping portions or remove entire intervals.

Example Input

cat example_a.bed

chr1	100	200	gene1	100	+
chr1	150	250	gene2	200	-
chr1	400	500	gene3	300	+
chr2	100	300	gene4	400	+
chr2	500	700	gene5	500	-

cat example_b.bed

chr1	120	180	feat1	50	+
chr1	220	280	feat2	60	-
chr1	450	480	feat3	70	+
chr2	150	250	feat4	80	+
chr2	600	650	feat5	90	-

Command

grit subtract -a example_a.bed -b example_b.bed

Output

chr1	100	120	gene1	100	+
chr1	180	200	gene1	100	+
chr1	180	220	gene2	200	-
chr1	400	450	gene3	300	+
chr1	480	500	gene3	300	+
chr2	100	150	gene4	400	+
chr2	250	300	gene4	400	+
chr2	500	600	gene5	500	-
chr2	650	700	gene5	500	-

Options

Flag	Description
-a, --file-a	Input BED file A
-b, --file-b	Input BED file B
-A, --remove-entire	Remove entire A feature if any overlap
-f, --fraction	Minimum overlap fraction required
-r, --reciprocal	Require reciprocal fraction overlap
--streaming	Use streaming mode (O(k) memory)
--assume-sorted	Skip sorted validation
--stats	Print streaming statistics

Remove Entire Features

Remove complete intervals that have any overlap:

grit subtract -a example_a.bed -b example_b.bed -A

Streaming Mode

grit subtract -a example_a.bed -b example_b.bed --streaming --assume-sorted

Notes

• Default behavior trims overlapping portions
• Use -A to remove entire intervals with any overlap
• Streaming mode uses O(k) memory where k = max overlapping intervals