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

# 2) Keep both records plus overlap length
intersectBed \
  -a peaks.bed \
  -b promoters.bed \
  -wa -wb -wo

# 3) Count overlaps per A interval with reciprocal overlap filtering
intersectBed \
  -a peaks.bed \
  -b enhancers.bed \
  -c \
  -f 0.5 \
  -r

Recommended Workflow

1. Decide whether you need filtering (-u, -v), joining (-wa, -wb, -wo, -wao, -loj), or counting (-c, -C) before you run the command.
2. Confirm chromosome naming conventions match across files before trusting an empty result.
3. Add -s / -S and -f / -F / -r / -e deliberately instead of assuming bedtools defaults fit the biology.
4. Use -sorted only when the inputs are truly sorted, and provide -g if you need a fixed chromosome order.

Guardrails

• Both -a and -b are required, and -b can contain multiple files or wildcards.
• With BAM as -a, the default output is BAM-like alignment output unless you request -bed or -ubam.
• -wao reports non-overlapping A records with a NULL B feature and overlap 0; -wo does not.
• -C reports counts per B file on distinct lines, which is easy to misread if you expected one line per A feature.
• Prefer -h for help; some --help / --version patterns on these bedtools wrappers emit errors before exiting.