bedtools/bedtools_multicov

genomics

coverage

bam

alignment

multi-sample

depth

sequencing

Description

Count sequence coverage for multiple BAM files at specific genomic loci.

bedtools multicov counts the number of alignments from multiple BAM files that overlap
each interval in a BED/GFF/VCF file. For each genomic interval, it reports the coverage
from each BAM file in additional columns, making it ideal for comparing coverage across
multiple samples or conditions.

This tool is commonly used for:

Multi-sample coverage analysis across specific regions
Comparing read depths between different samples
Quality control of sequencing experiments
Preparing coverage data for differential analysis
Generating coverage matrices for downstream analysis

Type

bash_script

License

MIT

Keywords

genomics

coverage

bam

alignment

multi-sample

depth

sequencing

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.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_multicov/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--bams -bams	file required multiple	Input BAM files for coverage counting. Format: Sorted and indexed BAM files Content: Aligned sequencing reads Usage: Coverage will be calculated for each BAM file separately Requirements: Must be coordinate-sorted with corresponding .bai index files Output: Each BAM contributes one column to the output
--bed -bed	file required	BED/GFF/VCF file with genomic intervals for coverage calculation. Format: BED, GFF, or VCF file with genomic coordinates Content: Intervals where coverage will be measured Usage: Each interval becomes a row in the output with coverage columns appended Requirements: Chromosome names must match BAM file references

Name

Type & Properties

--bams

-bams

file

required

multiple

--bed

-bed

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with coverage counts appended to input intervals. Format: Same as input BED/GFF/VCF with additional coverage columns Content: Original interval data plus one coverage column per BAM file Columns: Coverage counts are appended in the order BAM files were specified

Name

Type & Properties

--output

file

required

output

Overlap Options

Name	Type & Properties	Description
--min_overlap -f	double	Minimum overlap required as a fraction of each BED interval. Default: 1E-9 (essentially 1 base pair) Range: 0.0 to 1.0 Usage: Read must overlap at least this fraction of the interval Example: 0.5 requires read to overlap at least 50% of interval
--reciprocal -r	boolean_true	Require reciprocal overlap for both interval and read. Usage: Both interval and read must overlap each other by min_overlap fraction Example: With -f 0.9, interval must overlap 90% of read AND read must overlap 90% of interval Effect: More stringent overlap requirement than -f alone Default: false (only interval overlap required)

Name

Type & Properties

--min_overlap

-f

double

--reciprocal

-r

boolean_true

Strand Options

Name	Type & Properties	Description
--same_strand -s	boolean_true	Only count reads on the same strand as the interval. Usage: Requires strand information in BED file (6th column) Effect: Ignores reads on opposite strand Applications: Strand-specific RNA-seq analysis, antisense detection Default: false (count reads on both strands)
--opposite_strand -S	boolean_true	Only count reads on the opposite strand from the interval. Usage: Requires strand information in BED file (6th column) Effect: Ignores reads on same strand Applications: Antisense RNA detection, strand-specific analysis Default: false (count reads on both strands)

Name

Type & Properties

--same_strand

-s

boolean_true

--opposite_strand

-S

boolean_true

Read Filtering

Name	Type & Properties	Description
--min_quality -q	integer	Minimum mapping quality (MAPQ) required for reads. Default: 0 (no quality filtering) Range: 0-255 Usage: Higher values exclude poorly mapped reads Common values: 10, 20, 30 for increasingly stringent filtering
--include_duplicates -D	boolean_true	Include duplicate reads in coverage counting. Default: false (exclude duplicates) Usage: Count reads marked as duplicates in BAM FLAG field Applications: When duplicates represent real biological signal Effect: May increase coverage counts significantly
--include_failed_qc -F	boolean_true	Include reads that failed quality control checks. Default: false (exclude failed QC reads) Usage: Count reads marked as QC failures in BAM FLAG field Applications: When QC failures should still be counted Effect: May include low-quality alignments
--proper_pairs_only -p	boolean_true	Only count reads from proper pairs. Default: false (count all alignments above quality threshold) Usage: Requires both reads in pair to be properly aligned Applications: Paired-end sequencing quality control Effect: Excludes singleton reads and improperly paired reads

Name

Type & Properties

--min_quality

-q

integer

--include_duplicates

-D

boolean_true

--include_failed_qc

-F

boolean_true

--proper_pairs_only

-p

boolean_true

Advanced Options

Name	Type & Properties	Description
--split	boolean_true	Treat split BAM or BED12 entries as distinct intervals. BAM context: Count spliced alignments across individual exons BED12 context: Process each block in BED12 entry separately Applications: RNA-seq analysis, exon-specific coverage Default: false (treat as single interval)

Name

Type & Properties

--split

boolean_true