subtract-bed

name	subtract-bed
description	Use when you need to remove overlapping portions of one interval set from another, such as subtracting blacklist, repeat, or annotation regions from BED, GFF, VCF, or BAM-like inputs.
disable-model-invocation	true
user-invocable	true

subtract-bed

Quick Start

• Command: subtractBed -a <bed/gff/vcf> -b <bed/gff/vcf>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/subtractBed
• Full reference: references/help.md

When To Use This Tool

• Remove blacklist, repeat, or exclusion intervals from a target interval set.
• Trim only the overlapping segments from A while keeping the remaining pieces.
• Drop entire A features on qualifying overlap with -A or -N.
• Apply strand-aware and fraction-aware subtraction rules before downstream counting or annotation.

Common Patterns

# 1) Remove blacklist segments from peaks
subtractBed \
  -a peaks.bed \
  -b blacklist.bed \
  > peaks.clean.bed

# 2) Remove whole A features if at least half the feature overlaps B
subtractBed \
  -a exons.bed \
  -b repeats.bed \
  -A \
  -f 0.5 \
  > exons.filtered.bed