bedtools/bedtools_fisher

genomics

intervals

fisher

statistics

overlap

significance

test

Description

Calculate Fisher's exact test statistic between two feature files.

This tool performs Fisher's exact test to assess the statistical significance
of overlaps between genomic intervals in two files. It calculates the probability
of observing the given overlap pattern by chance, providing a p-value for
statistical inference.

Type

bash_script

License

MIT

Keywords

genomics

intervals

fisher

statistics

overlap

significance

test

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_fisher/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input_a -a	file required	First input file for comparison. Format: BED, GFF, VCF file with genomic intervals Requirement: Must be sorted by chromosome, then start position Usage: File A for Fisher's exact test comparison
--input_b -b	file required	Second input file for comparison. Format: BED, GFF, VCF file with genomic intervals Requirement: Must be sorted by chromosome, then start position Usage: File B for Fisher's exact test comparison
--genome -g	file required	Genome file defining chromosome sizes. Format: Tab-delimited file with chromosome name and size Purpose: Enforces consistent chromosome sort order Example: chr1\t249250621

Name

Type & Properties

--input_a

-a

file

required

--input_b

-b

file

required

--genome

-g

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with Fisher's exact test results. Contains statistical results including p-values for overlap significance between input files.

Name

Type & Properties

--output

file

required

output

Overlap Options

Name	Type & Properties	Description
--merge_overlaps -m	boolean_true	Merge overlapping intervals before analysis. Effect: Collapses overlapping intervals in both files Usage: Prevents double-counting of overlapping features Default: false (no merging)
--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 both A and B. Effect: Both -f and -F thresholds must be satisfied 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

--merge_overlaps

-m

boolean_true

--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 report overlaps on the same strand Default: false (strand-independent)
--opposite_strand -S	boolean_true	Require different strandedness for overlaps. Effect: Only report overlaps on opposite strands Default: false (strand-independent)

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
--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

--no_name_check

--nonamecheck

boolean_true

--no_buffer

--nobuf

boolean_true

--io_buffer

--iobuf

string