multiinter

Description

Identify common intervals across multiple BED files. Reports regions and which files contain them.

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 multiinter -i example_a.bed example_b.bed

Output

chr1	100	120	1	1	1	0
chr1	120	150	2	1,2	1	1
chr1	150	180	2	1,2	1	1
chr1	180	200	1	1	1	0
chr1	200	220	1	1	1	0
chr1	220	250	2	1,2	1	1
chr1	250	280	1	2	0	1
chr1	400	450	1	1	1	0
chr1	450	480	2	1,2	1	1
chr1	480	500	1	1	1	0
chr2	100	150	1	1	1	0
chr2	150	250	2	1,2	1	1
chr2	250	300	1	1	1	0
chr2	500	600	1	1	1	0
chr2	600	650	2	1,2	1	1
chr2	650	700	1	1	1	0

Output columns: chrom, start, end, file count, file list, presence flags for each file.

Options

Flag	Description
-i, --input	Input BED files (multiple allowed)
--cluster	Only output intervals found in all files

Cluster Mode

Only report intervals present in ALL files:

grit multiinter -i example_a.bed example_b.bed --cluster

Multiple Files

grit multiinter -i file1.bed file2.bed file3.bed file4.bed

Notes

• Useful for finding consensus regions across samples
• File numbering starts at 1
• Cluster mode filters to intervals present in every input file