grit intersect

Find overlapping intervals between two BED files.

Usage

grit intersect [OPTIONS] -a <FILE_A> -b <FILE_B>

Options

Option	Description
-a, --file-a <FILE>	Input BED file A
-b, --file-b <FILE>	Input BED file B
--wa	Write original A entry
--wb	Write original B entry
-u, --unique	Only report unique A intervals
-v, --no-overlap	Only report A intervals with NO overlap
-f, --fraction <F>	Minimum overlap fraction for A (0.0-1.0)
-r, --reciprocal	Require reciprocal fraction overlap
-c, --count	Report the number of overlaps
--streaming	Use streaming mode (constant memory)
--assume-sorted	Skip sorted validation
--allow-unsorted	Allow unsorted input (uses O(n) memory)
-g, --genome <FILE>	Genome file for chromosome order validation

Examples

Basic intersection

# Find overlapping regions
grit intersect -a regions.bed -b reads.bed > overlaps.bed

# Streaming mode for large files
grit intersect -a regions.bed -b reads.bed --streaming --assume-sorted

Report original entries

# Report original A entry for each overlap
grit intersect -a genes.bed -b peaks.bed --wa > results.bed

# Report both A and B entries
grit intersect -a genes.bed -b peaks.bed --wa --wb > results.bed

Unique intervals

# Only report each A interval once
grit intersect -a genes.bed -b reads.bed -u > unique_genes.bed

Find non-overlapping intervals

# Report A intervals that DON'T overlap with B
grit intersect -a all_regions.bed -b excluded.bed -v > remaining.bed

Minimum overlap fraction

# Require at least 50% overlap
grit intersect -a genes.bed -b reads.bed -f 0.5 > significant_overlaps.bed

# Require reciprocal 50% overlap (both A and B must overlap 50%)
grit intersect -a set1.bed -b set2.bed -f 0.5 -r > reciprocal.bed

Count overlaps

# Count how many B intervals overlap each A interval
grit intersect -a genes.bed -b reads.bed -c > counts.bed

Output

Default output (intersection coordinates):

chr1    150    200

With –wa –wb (both entries):

chr1    100    200    chr1    150    250

With -c (counts):

chr1    100    200    5

Performance

For large files, use streaming mode:

# Fastest: streaming with pre-sorted input
grit intersect -a sorted_a.bed -b sorted_b.bed --streaming --assume-sorted

Mode	Memory	Requirements
Streaming	O(k)	Sorted input
Default	O(n)	Any input

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