grit multiinter

Identify common intervals across multiple BED files.

Usage

grit multiinter [OPTIONS] -i <FILE1> <FILE2> [FILE3...]

Options

Option	Description
-i, --input <FILES>	Input BED files (2 or more)
--cluster	Only output intervals found in all files
--streaming	Use streaming mode (O(k) memory)
--assume-sorted	Skip sorted validation

Examples

Basic multi-intersection

# Find common regions across 3 files
grit multiinter -i file1.bed file2.bed file3.bed > common.bed

# Streaming mode for large files
grit multiinter -i *.bed --streaming --assume-sorted > common.bed

Intervals in ALL files

# Only report intervals present in every file
grit multiinter -i rep1.bed rep2.bed rep3.bed --cluster > consensus.bed

Compare replicates

# Find consensus peaks across replicates
grit multiinter -i rep1_peaks.bed rep2_peaks.bed rep3_peaks.bed --cluster > consensus_peaks.bed

Compare conditions

# Find regions present in all samples
grit multiinter -i sample1.bed sample2.bed sample3.bed sample4.bed > multi.bed

Output

Default output:

chr1    100    150    2    1,2
chr1    150    200    3    1,2,3
chr1    200    250    1    3

Column	Description
1-3	Chromosome, start, end
4	Number of files with this interval
5	List of file indices (1-based)

With –cluster:

chr1    150    200    3    1,2,3

Only intervals present in ALL files are reported.

Visual Example

File 1:  |--------|
File 2:      |--------|
File 3:          |--------|

Output:
         |--|              (in file 1 only)
             |--|          (in files 1,2)
                 |--|      (in files 1,2,3)  ← --cluster reports only this
                     |--|  (in files 2,3)
                         |-| (in file 3 only)

Use Cases

Consensus peaks

# Require peak in at least 2 of 3 replicates
grit multiinter -i rep1.bed rep2.bed rep3.bed | awk '$4 >= 2' > consensus.bed

Universal binding sites

# Sites bound in ALL cell types
grit multiinter -i cellA.bed cellB.bed cellC.bed --cluster > universal.bed

Sample overlap analysis

# Analyze overlap patterns
grit multiinter -i *.bed > overlap_matrix.bed

Performance

# Fastest with streaming mode
grit multiinter -i *.bed --streaming --assume-sorted > result.bed

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