bedtools/bedtools_multiinter
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
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 |
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 |
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 |
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 Relationships
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