jaccard
Description
Calculate Jaccard similarity between two BED files. Measures the overlap between two interval sets.
chr1 100 200 gene1 100 +
chr1 150 250 gene2 200 -
chr1 400 500 gene3 300 +
chr2 100 300 gene4 400 +
chr2 500 700 gene5 500 -
chr1 120 180 feat1 50 +
chr1 220 280 feat2 60 -
chr1 450 480 feat3 70 +
chr2 150 250 feat4 80 +
chr2 600 650 feat5 90 -
Command
grit jaccard -a example_a.bed -b example_b.bed
Output
intersection union jaccard n_intersections
270 680 0.397059 5
Options
| Flag | Description |
-a, --file-a | Input BED file A |
-b, --file-b | Input BED file B |
Output Columns
| Column | Description |
| intersection | Total bases in intersection |
| union | Total bases in union |
| jaccard | Jaccard index (intersection / union) |
| n_intersections | Number of intersecting interval pairs |
Notes
- Jaccard index ranges from 0 (no overlap) to 1 (identical)
- Useful for comparing interval set similarity
- Both files are merged internally before comparison