bedtools/bedtools_summary
Description
Report summary statistics of genomic intervals in a file.
bedtools summary analyzes genomic intervals and provides comprehensive statistics
including total number of features, total length covered, average feature size,
and other descriptive metrics. This tool is essential for quality control and
exploratory data analysis of genomic datasets, helping researchers understand
the distribution and characteristics of their interval data.
This tool is commonly used for:
Quality control assessment of genomic interval datasets
Exploratory data analysis of ChIP-seq peaks, gene annotations, or variant calls
Comparative analysis of interval characteristics between samples
Data preprocessing and validation before downstream analysis
Generating summary reports for genomic studies
Statistical characterization of genomic features
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input file containing genomic intervals for statistical analysis. **Format:** BED, GFF, VCF, or BAM file with genomic coordinates **Content:** Genomic intervals to be analyzed for summary statistics **Usage:** Each interval contributes to the overall statistical summary **Requirements:** Standard genomic interval format with chromosome, start, end coordinates **Analysis:** Statistics computed across all intervals in the file |
--genome -g | file required | Genome file with chromosome names and lengths. **Format:** Tab-delimited file with chromosome names and sizes **Structure:** Each line contains: <chromName><TAB><chromSize> **Purpose:** Provides reference genome context for statistical calculations **Example lines:** "chr1\t249250621" or "chr2\t243199373" **Usage:** Used to calculate genome coverage percentages and context statistics |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Output file with summary statistics of the genomic intervals. **Format:** Tab-delimited text file with statistical metrics **Content:** Comprehensive summary including count, total length, average size, etc. **Columns:** Various statistical measures of the interval dataset **Usage:** Results suitable for further analysis or reporting |
Analysis Options
Name | Type & Properties | Description |
|---|
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_summary/main.nf \
-params-file params.yaml Relationships
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