bedtools/bedtools_coverage

genomics

intervals

coverage

depth

breadth

overlap

statistics

Description

Calculate coverage of genomic intervals from one file over intervals in another.

This tool reports the depth and breadth of coverage of features from file B
over the intervals in file A. It provides detailed coverage statistics including
overlap counts, covered bases, and coverage fractions.

Type

bash_script

License

MIT

Keywords

genomics

intervals

coverage

depth

breadth

overlap

statistics

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 v0.4.1 \  
  -main-script target/nextflow/bedtools/bedtools_coverage/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input_a -a	file required	Query intervals file in BED, GFF, or VCF format. Purpose: Intervals for which coverage will be calculated BED format: Standard genomic interval format GFF format: Gene feature format with annotations VCF format: Variant call format
--input_b -b	file required multiple	Coverage source file(s) in BED, GFF, VCF, or BAM format. Purpose: Features that provide coverage over query intervals Multiple files: Can specify multiple coverage sources BAM support: Binary alignment files for sequencing coverage

Name

Type & Properties

--input_a

-a

file

required

--input_b

-b

file

required

multiple

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with coverage statistics. Default output: For each interval in A, reports: 1. Number of overlapping features from B 2. Number of bases in A with non-zero coverage 3. Length of interval in A 4. Fraction of bases in A with non-zero coverage

Name

Type & Properties

--output

file

required

output

Coverage Reporting

Name	Type & Properties	Description
--histogram -hist	boolean_true	Report coverage histogram for each feature and summary. Output format: depth, bases at depth, feature size, percentage Use case: Detailed coverage distribution analysis
--depth_per_position -d	boolean_true	Report depth at each position in each interval. Output: One-based positions with coverage depth Use case: Position-specific coverage analysis Note: Generates large output for long intervals
--counts_only -counts	boolean_true	Only report overlap counts, no fractions. Simplified output: Just the number of overlapping features Use case: When only overlap counts are needed
--mean_depth -mean	boolean_true	Report mean coverage depth for each interval. Output: Average depth across all positions in interval Use case: Summary coverage statistics

Name

Type & Properties

--histogram

-hist

boolean_true

--depth_per_position

-d

boolean_true

--counts_only

-counts

boolean_true

--mean_depth

-mean

boolean_true

Strand Options

Name	Type & Properties	Description
--same_strand -s	boolean_true	Require same strandedness for overlaps. Default: Overlaps reported regardless of strand When enabled: Only count overlaps on same strand
--different_strand -S	boolean_true	Require different strandedness for overlaps. Default: Overlaps reported regardless of strand When enabled: Only count overlaps on opposite strand

Name

Type & Properties

--same_strand

-s

boolean_true

--different_strand

-S

boolean_true

Overlap Requirements

Name	Type & Properties	Description
--min_overlap_a -f	double	Minimum overlap required as fraction of A. Range: 0.0 to 1.0 Default: 1E-9 (essentially 1bp) Example: 0.50 requires 50% of A to be overlapped
--min_overlap_b -F	double	Minimum overlap required as fraction of B. Range: 0.0 to 1.0 Default: 1E-9 (essentially 1bp) Example: 0.80 requires 80% of B to overlap A
--reciprocal -r	boolean_true	Require reciprocal minimum fraction for A AND B. Requires: Both -f and -F fractions to be satisfied Use case: Stringent overlap requirements
--either -e	boolean_true	Require minimum fraction for A OR B (not both). Default: Both -f and -F must be satisfied When enabled: Either fraction requirement is sufficient

Name

Type & Properties

--min_overlap_a

-f

double

--min_overlap_b

-F

double

--reciprocal

-r

boolean_true

--either

-e

boolean_true

Format Options

Name	Type & Properties	Description
--split	boolean_true	Treat split BAM/BED12 entries as distinct intervals. BAM: Handle spliced alignments as separate blocks BED12: Process each block independently
--bed_output -bed	boolean_true	Write output in BED format when using BAM input. Default: BAM input produces BAM-style output When enabled: Force BED format output
--header	boolean_true	Print header from input A file before results. Use case: Preserve metadata from input file

Name

Type & Properties

--split

boolean_true

--bed_output

-bed

boolean_true

--header

boolean_true

Performance Options

Name	Type & Properties	Description
--sorted	boolean_true	Use chromsweep algorithm for sorted input. Requirements: Input must be sorted by chromosome and position Performance: Faster processing for large files
--genome -g	file	Genome file for consistent chromosome ordering. Format: Tab-delimited chromosome names and sizes Use case: Ensure consistent sort order with -sorted option
--no_name_check -nonamecheck	boolean_true	Don't error on different chromosome naming conventions. Example: Allows mixing "chr1" and "chr01" Use case: Working with files from different sources

Name

Type & Properties

--sorted

boolean_true

--genome

-g

file

--no_name_check

-nonamecheck

boolean_true