bedtools/bedtools_summary

genomics

intervals

statistics

summary

analysis

quality-control

metrics

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

Type

bash_script

License

MIT

Keywords

genomics

intervals

statistics

summary

analysis

quality-control

metrics

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.txt"  
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_summary/main.nf \  
  -params-file params.yaml

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

Name

Type & Properties

--input

-i

file

required

--genome

-g

file

required

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

Name

Type & Properties

--output

file

required

output

Analysis Options

Name

Type & Properties