Comparing Peak Caller Outputs

Use the BED comparator for ATAC-seq, ChIP-seq, and other interval outputs:

pipeconcord compare peaks_a.bed peaks_b.bed --type bed

The comparator assumes standard BED 0-based half-open intervals and reports:

• base-pair Jaccard
• reciprocal bp coverage
• interval precision, recall, and F1
• interval length and count similarity

Set a reciprocal overlap threshold when small edge overlaps should not count as matching intervals:

pipeconcord compare peaks_a.bed peaks_b.bed \
  --type bed \
  --min-reciprocal-overlap 0.5