grit slop

Extend intervals by a given number of bases.

Usage

grit slop [OPTIONS] -i <INPUT> -g <GENOME>

Options

Option	Description
-i, --input <FILE>	Input BED file
-g, --genome <FILE>	Genome file (chromosome sizes)
-b, --both <N>	Extend both sides by N bases
-l, --left <N>	Extend left side by N bases
-r, --right <N>	Extend right side by N bases
-s, --strand	Use strand info (left=upstream, right=downstream)
--pct	Interpret values as fraction of interval size

Examples

Extend both sides

# Extend each interval by 100bp on both sides
grit slop -i regions.bed -g genome.txt -b 100 > extended.bed

# Extend by 1kb
grit slop -i peaks.bed -g genome.txt -b 1000 > peaks_1kb.bed

Asymmetric extension

# Extend 500bp left, 200bp right
grit slop -i genes.bed -g genome.txt -l 500 -r 200 > extended.bed

Strand-aware extension

# Extend 1kb upstream, 500bp downstream (strand-aware)
grit slop -i genes.bed -g genome.txt -l 1000 -r 500 -s > extended.bed

Percentage-based extension

# Extend by 10% of interval size on each side
grit slop -i regions.bed -g genome.txt -b 0.1 --pct > extended.bed

# Double the interval size (50% each side)
grit slop -i regions.bed -g genome.txt -b 0.5 --pct > doubled.bed

Genome File Format

The genome file specifies chromosome sizes:

chr1    248956422
chr2    242193529
chr3    198295559
chrX    156040895
chrY    57227415

Create from a FASTA index:

cut -f1,2 genome.fa.fai > genome.txt

Output

Input:

chr1    100    200

With -b 50:

chr1    50    250

Note: Coordinates are clamped to chromosome boundaries (0 to chrom_size).

Visual Example

Original:           |--------|
With -b 100:  |-----|--------|-----|
              ^100bp         ^100bp

With -l 200 -r 50:
             |------|--------|--|
             ^200bp          ^50bp

Use Cases

Promoter regions

# Get 2kb upstream of TSS
grit slop -i tss.bed -g genome.txt -l 2000 -r 0 -s > promoters.bed

Peak extension

# Extend ChIP-seq peaks by 250bp
grit slop -i peaks.bed -g genome.txt -b 250 > extended_peaks.bed

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