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.
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 |
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. |
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 |
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 v0.4.1 \
-main-script target/nextflow/bedtools/bedtools_complement/main.nf \
-params-file params.yaml Relationships
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Current component
bedtools/bedtools_complementbiobox v0.4.1
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