bedtools/bedtools_complement

genomics

intervals

complement

gaps

uncovered

background

Description

Find genomic intervals that are NOT covered by input intervals.

This tool returns the complement of genomic intervals - the regions
of the genome that are NOT covered by the input features. Useful for
finding gaps, uncovered regions, or background intervals.

Type

bash_script

License

MIT

Keywords

genomics

intervals

complement

gaps

uncovered

background

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"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/bedtools/bedtools_complement/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input file in BED, GFF, or VCF format. BED format: Standard genomic interval format GFF format: Gene feature format with annotations VCF format: Variant call format Requirements: Should be sorted by chromosome and position for optimal performance
--genome -g	file required	Genome file defining chromosome names and sizes. Format: Tab-delimited file with chromosome name and size Example line: chr1 249250621 Sources: Can be created with samtools faidx or UCSC Table Browser Purpose: Defines the complete genomic space for complement calculation

Name

Type & Properties

--input

-i

file

required

--genome

-g

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with complement intervals. Contains genomic intervals representing the regions NOT covered by the input intervals. Output is in BED format with chromosome, start, and end coordinates.

Name

Type & Properties

--output

file

required

output

Options

Name	Type & Properties	Description
--limit_chromosomes -L	boolean_true	Limit output to chromosomes present in input file. Default: Output includes all chromosomes from genome file When enabled: Only output complement for chromosomes that have records in the input file Use case: Focus analysis on chromosomes of interest

Name

Type & Properties

--limit_chromosomes

-L

boolean_true