bedtools/bedtools_multiinter

genomics

intervals

intersection

multi-file

bed

gff

vcf

consensus

Description

Identify common intervals among multiple BED/GFF/VCF files.

bedtools multiinter finds regions that are shared across multiple interval files and
reports statistics about the overlaps. It can identify intervals that are present in
all files, some files, or generate a matrix showing which intervals are found in which files.

This tool is commonly used for:

Finding consensus regions across multiple datasets
Identifying tissue-specific or condition-specific intervals
Creating intersection matrices for comparative analysis
Merging annotations from multiple sources
Quality control of peak calling across replicates

Type

bash_script

License

MIT

Keywords

genomics

intervals

intersection

multi-file

bed

gff

vcf

consensus

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.bed"  
filler: [ "0" ]  
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_multiinter/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required multiple	Input BED/GFF/VCF files to intersect. Format: BED, GFF, or VCF files with genomic coordinates Content: Intervals to find intersections between Requirements: Each file must be sorted by chromosome and start position Usage: Intersections will be calculated across all provided files Output: Results show which intervals are shared between files

Name

Type & Properties

--input

-i

file

required

multiple

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with intersection results. Format: Tab-delimited file showing intersection statistics Content: Intervals and which files they appear in Columns: Chromosome, start, end, plus indicator columns for each input file

Name

Type & Properties

--output

file

required

output

Options

Name	Type & Properties	Description
--cluster	boolean_true	Invoke Ryan Layer's clustering algorithm. Effect: Uses advanced clustering for overlapping intervals Usage: Alternative algorithm for intersection detection Default: false (uses standard intersection algorithm)
--header	boolean_true	Print a header line with column names. Content: Chromosome, start, end plus names of each input file Usage: Makes output easier to interpret and parse Default: false (no header printed)
--names	string multiple	List of names to describe each input file. Format: One name per input file, in the same order Usage: These names appear in the header line (requires --header) Length: Must match the number of input files Default: Files are numbered sequentially if not provided
--genome -g	file	Genome file for calculating empty regions. Format: Tab-delimited file with chromosome names and lengths Content: One line per chromosome: <chrom_name><tab><chrom_length> Usage: Required for --empty option to work Purpose: Defines chromosome boundaries for empty region calculation
--empty	boolean_true	Report empty regions without values in all files. Requirements: Must be used with --genome option Purpose: Shows intervals where no input files have overlapping features Usage: Useful for finding gaps in coverage across all datasets Default: false (only reports regions with overlaps)
--filler	string	Text to use when representing intervals with no value. Default: "0" Usage: Customize the placeholder for empty intersections Examples: "N/A", ".", "NULL" Context: Appears in output when intervals have no overlapping features

Name

Type & Properties

--cluster

boolean_true

--header

boolean_true

--names

string

multiple

--genome

-g

file

--empty

boolean_true

--filler

string