slop-bed

name	slop-bed
description	Use when you need to expand genomic intervals by adding flanking base pairs to features in BED, GFF, or VCF files.
disable-model-invocation	true
user-invocable	true

slop-bed

Quick Start

• Command: slopBed -i <input> -g <genome> -b <int> or bedtools slop -i <input> -g <genome> -b <int>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/slopBed
• Full reference: See references/help.md

When To Use This Tool

• Expand intervals outward by a fixed amount on both sides.
• Add asymmetric upstream/downstream flanks with -l and -r.
• Build strand-aware promoter or neighborhood windows with -s.
• Scale flanking size as a fraction of interval length with -pct.

Common Patterns

# 1) Add 200 bp of symmetric flank to every interval
slopBed \
  -i peaks.bed \
  -g genome.sizes \
  -b 200

# 2) Create a strand-aware promoter window: 2 kb upstream, 200 bp downstream
slopBed \
  -i transcripts.bed \
  -g genome.sizes \
  -l 2000 \
  -r 200 \
  -s

# 3) Expand each interval by 25% of its own length on both sides
slopBed \
  -i intervals.bed \
  -g genome.sizes \
  -b 0.25 \
  -pct

Recommended Workflow

1. Prepare a genome file (or FASTA .fai) so bedtools knows the chromosome bounds.
2. Choose symmetric expansion with -b or asymmetric expansion with -l plus -r.
3. Add -s only when left/right should be interpreted relative to feature strand, and add -pct only when flank sizes should scale with feature length.
4. Inspect a few results to confirm the biological interpretation and the expected boundary clipping at chromosome edges.

Guardrails

• -i and -g are both required.
• Use either -b alone or -l together with -r; these modes are mutually exclusive.
• With -pct, values are fractions of feature length rather than base pairs.
• -s changes how left and right are interpreted for negative-strand records; it is essential for true upstream/downstream flanks.
• Starts are clipped to 0 and ends are clipped to chromosome length when expansion would cross chromosome boundaries.