To compute the consensus overlapping regions across your three histone mark peak files (H3K4me3, H3K27ac, H3K27me3) while handling partial overlaps, expansions, and separating regions by coverage (e.g., unique, pairwise, all-three like in your images), skip manual pairwise merging/intersection. Use bedtools multiinter directly on all three sorted BED files—it automatically splits into disjoint minimal regions and annotates coverage from each input.

Step 1: Run multiinter

Assume your sorted peak files are h3k4me3_peaks.bed, h3k27ac_peaks.bed, and h3k27me3_peaks.bed (chrom/start/end format; sort them first with sort -k1,1 -k2,2n if needed).

bedtools multiinter -i h3k4me3_peaks.bed h3k27ac_peaks.bed h3k27me3_peaks.bed > consensus_regions.bed

• Output columns: chrom, start, end, h3k4me3_coverage (0/1), h3k27ac_coverage (0/1), h3k27me3_coverage (0/1).
• Regions are non-overlapping; coverage=1 means fully covered by that mark's peak(s).
• This captures your "false overlaps" by only counting true intersections (ignores expansions unless they truly overlap).

Step 2: Separate regions by consensus (e.g., via awk)

Filter for desired categories (adjust column numbers if your BED has extra columns):

• All three marks (100% consensus overlap):

  awk '($4==1 && $5==1 && $6==1)' consensus_regions.bed > all_three.bed
  

• H3K4me3 + H3K27ac only (no H3K27me3):

  awk '($4==1 && $5==1 && $6==0)' consensus_regions.bed > me3_ac_only.bed
  

• H3K4me3 + H3K27me3 only:

  awk '($4==1 && $5==0 && $6==1)' consensus_regions.bed > me3_me3m_only.bed
  

• H3K27ac + H3K27me3 only:

  awk '($4==0 && $5==1 && $6==1)' consensus_regions.bed > ac_me3m_only.bed
  

• H3K4me3 only:

  awk '($4==1 && $5==0 && $6==0)' consensus_regions.bed > me3_only.bed
  

• H3K27ac only:

  awk '($4==0 && $5==1 && $6==0)' consensus_regions.bed > ac_only.bed
  

• H3K27me3 only:

  awk '($4==0 && $5==0 && $6==1)' consensus_regions.bed > me3m_only.bed
  

• No coverage (ignore):

  awk '($4==0 && $5==0 && $6==0)' consensus_regions.bed > none.bed  # Usually empty
  

Notes

• No need for -f 1.0 or -wa/-wb/-wao hacks—the coverage columns handle "100% overlap" per region.
• If peaks are expanded too much, consider shrinking them first: bedtools slop -i peaks.bed -g genome.sizes -b -50 (adjust -50 to contract by 50bp).
• For your pairwise merge issue in A: multiinter on just two files gives the union/split directly (e.g., -i me3.bed ac.bed), but doing all three avoids extra steps.
• Visualize in IGV/UCSC to match your images.

This should give clean, separated regions without false positives. If you share sample BED snippets, I can refine.