bedtools/bedtools_jaccard

genomics

intervals

jaccard

similarity

statistics

overlap

intersection

union

Description

Calculate Jaccard similarity statistic between two genomic feature files.

The Jaccard index measures similarity between finite sample sets, defined as
the size of the intersection divided by the size of the union. Values range
from 0 (no intersection) to 1 (identical sets). This tool calculates the
Jaccard statistic for genomic intervals, providing a quantitative measure
of overlap between two interval sets.

Type

bash_script

License

MIT

Keywords

genomics

intervals

jaccard

similarity

statistics

overlap

intersection

union

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.txt"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.0 \  
  -main-script target/nextflow/bedtools/bedtools_jaccard/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input_a -a	file required	First input file for Jaccard comparison. Format: BED, GFF, VCF file with genomic intervals Requirement: Must be sorted by chromosome, then start position Usage: File A for Jaccard similarity calculation
--input_b -b	file required	Second input file for Jaccard comparison. Format: BED, GFF, VCF file with genomic intervals Requirement: Must be sorted by chromosome, then start position Usage: File B for Jaccard similarity calculation

Name

Type & Properties

--input_a

-a

file

required

--input_b

-b

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with Jaccard similarity statistics. Format: Tab-delimited with intersection, union, and Jaccard values Columns: intersection, union, jaccard Range: Jaccard values from 0.0 to 1.0

Name

Type & Properties

--output

file

required

output

Overlap Options

Name	Type & Properties	Description
--min_overlap_a -f	double	Minimum overlap required as fraction of A. Range: 0.0 to 1.0 Default: 1E-9 (effectively 1bp) Example: 0.50 requires 50% of A to be overlapped
--min_overlap_b -F	double	Minimum overlap required as fraction of B. Range: 0.0 to 1.0 Default: 1E-9 (effectively 1bp) Example: 0.50 requires 50% of B to be overlapped
--reciprocal -r	boolean_true	Require reciprocal overlap for A overlapping B. Requirement: Must be used solely with -f (min_overlap_a) Effect: Requires B overlaps specified fraction of A AND A overlaps same fraction of B Example: With -f 0.90 -r, requires B overlaps 90% of A AND A overlaps 90% of B Default: false
--either -e	boolean_true	Require minimum fraction satisfied for A OR B. Effect: Only one of -f or -F thresholds needs to be satisfied Alternative: Without -e, both fractions must be satisfied Default: false (both required)

Name

Type & Properties

--min_overlap_a

-f

double

--min_overlap_b

-F

double

--reciprocal

-r

boolean_true

--either

-e

boolean_true

Strand Options

Name	Type & Properties	Description
--same_strand -s	boolean_true	Require same strandedness for overlaps. Effect: Only consider overlaps on the same strand Default: false (strand-independent)
--opposite_strand -S	boolean_true	Require different strandedness for overlaps. Effect: Only consider overlaps on opposite strands Default: false (strand-independent) Note: May have issues in some bedtools versions requiring strand specification

Name

Type & Properties

--same_strand

-s

boolean_true

--opposite_strand

-S

boolean_true

Format Options

Name	Type & Properties	Description
--split	boolean_true	Treat split BAM or BED12 entries as distinct intervals. Effect: Split multi-block entries into individual intervals Usage: For BAM alignments with gaps or BED12 entries Default: false
--bed_output --bed	boolean_true	Write output in BED format when using BAM input. Effect: Forces BED output format for BAM inputs Default: false
--header	boolean_true	Print header from file A prior to results. Effect: Includes original header from input file A Default: false

Name

Type & Properties

--split

boolean_true

--bed_output

--bed

boolean_true

--header

boolean_true

Advanced Options

Name	Type & Properties	Description
--genome -g	file	Genome file for consistent chromosome sorting. Format: Tab-delimited file with chromosome name and size Usage: Only applies when used with sorted data Purpose: Enforces consistent chromosome sort order
--no_name_check --nonamecheck	boolean_true	Skip chromosome naming convention checks for sorted data. Effect: Allows different naming (e.g., "chr1" vs "chr01") Usage: For files with inconsistent chromosome naming Default: false (strict checking)
--no_buffer --nobuf	boolean_true	Disable buffered output. Effect: Print each line immediately instead of buffering Usage: For real-time processing or piping Trade-off: Slower performance but immediate output Default: false (buffered output)
--io_buffer --iobuf	string	Specify input buffer memory size. Format: Integer with optional K/M/G suffix Example: "128M" for 128 megabytes Note: No effect with compressed files

Name

Type & Properties

--genome

-g

file

--no_name_check

--nonamecheck

boolean_true

--no_buffer

--nobuf

boolean_true

--io_buffer

--iobuf

string