intersect-bed

name	intersect-bed
description	Use when you need to find overlaps between two genomic interval files (BED, GFF, VCF, or BAM), filter features by intersection, or count/report overlapping regions between datasets.
disable-model-invocation	true
user-invocable	true

intersect-bed

Quick Start

• Command: intersectBed -a <A> -b <B> [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/intersectBed
• Full reference: See references/help.md

When To Use This Tool

• Find overlaps between genomic intervals in BED, GFF, VCF, or BAM-like inputs.
• Filter A features to keep only overlapping records or only non-overlapping records.
• Count overlaps per A feature with -c / -C.
• Retain joined context from both files with -wa -wb, -wo, -wao, or -loj.
• Apply strand-aware and fraction-aware overlap rules before downstream annotation or QC.

Common Patterns

# 1) Basic interval overlap
intersectBed \
  -a peaks.bed \
  -b promoters.bed