flank-bed

name	flank-bed
description	Use when you need to create flanking intervals adjacent to BED/GFF/VCF features for promoter analysis, regulatory region discovery, or upstream/downstream sequence extraction.
disable-model-invocation	true
user-invocable	true

flank-bed

Quick Start

• Command: flankBed -i features.bed -g genome.txt [-b <size> | -l <size> -r <size>] [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/flankBed
• Full reference: See references/help.md

When To Use This Tool

• Create separate upstream and downstream flank intervals adjacent to existing features.
• Generate promoter-like or neighborhood windows around genes, peaks, or other annotations.
• Respect feature strand when translating left / right into upstream / downstream with -s.
• Define flank sizes as absolute bases or as a fraction of feature length with -pct.

Common Patterns

# 1) Symmetric 1 kb flanks on both sides
flankBed \
  -i genes.bed \
  -g genome.txt \
  -b 1000

# 2) Strand-aware upstream/downstream flanks
flankBed \
  -i genes.bed \
  -g genome.txt \
  -l 2000 \
  -r 500 \
  -s

# 3) Flanks sized as a fraction of feature length
flankBed \
  -i peaks.bed \
  -g genome.txt \
  -l 0.5 \
  -r 0.25 \
  -pct

Recommended Workflow

1. Decide whether you want symmetric flanks (-b) or distinct left / right sizes (-l and -r).
2. Add -s whenever left/right should be interpreted relative to biological strand.
3. Use -pct only when proportional flank size is the intended design.
4. Validate a few output records near chromosome starts and ends because flanks are clipped to genome boundaries.

Guardrails

• -i and -g are required.
• Use either -b alone or -l with -r; do not mix the modes.
• flankBed creates new adjacent intervals; it does not extend the original interval in place like slopBed.
• Starts are clamped to 0 and ends are clamped to chromosome length from the genome file.
• Prefer -h for help; GNU-style --help / --version calls on these wrappers are noisy.