bedtools/bedtools_genomecov

genome coverage

BED

GFF

VCF

BAM

depth

histogram

bedgraph

Description

Compute the coverage of a feature file among a genome.

Calculates genome-wide coverage statistics from BED, GFF, VCF, or BAM files.
Can produce coverage histograms, per-base depth, or BedGraph format output.

Inputs

Name	Type & Properties	Description
--input -i	file	Input genomic intervals file in BED, GFF, or VCF format. Supported formats: - BED format (standard genomic intervals) - GFF/GTF format (gene annotations) - VCF format (variant calls) Note: Required when not using `--input_bam`
--input_bam -ibam	file	Input BAM file for coverage calculation. Requirements: - BAM file must be sorted by position - When using BAM input, `--genome` option is ignored - Coordinates are determined from BAM header
--genome -g	file	Genome file defining chromosome names and sizes. Format: Two-column tab-delimited file: ``` chr1 248956422 chr2 242193529 ``` Note: Required when using `--input`, ignored when using `--input_bam`

Name

Type & Properties

--input

-i

file

--input_bam

-ibam

file

--genome

-g

file

Outputs

Name	Type & Properties	Description
--output	file required output	Output file containing coverage information. Output formats depend on options: - Default: Coverage histogram (depth vs count) - With `--depth`: Per-base depth (1-based coordinates) - With `--bed_graph`: BedGraph format for genome browsers

Name

Type & Properties

--output

file

required

output

Options

Name	Type & Properties	Description
--depth -d	boolean_true	Report the depth at each genome position with 1-based coordinates. Output format: `chromosome position depth` Default behavior: Reports coverage histogram instead
--depth_zero -dz	boolean_true	Report depth at each genome position with 0-based coordinates. Features: - Only reports positions with non-zero coverage - Uses 0-based coordinate system - More memory efficient than `--depth`
--bed_graph -bg	boolean_true	Report depth in BedGraph format for genome browser visualization. Output format: `chromosome start end depth` See [BedGraph specification](https://genome.ucsc.edu/goldenPath/help/bedgraph.html) for details.
--bed_graph_zero_coverage -bga	boolean_true	Report depth in BedGraph format including zero-coverage regions. Features: - Same as `--bed_graph` but includes regions with 0 coverage - Useful for finding uncovered regions: `grep -w 0$ output.bg` - Generates larger output files
--split	boolean_true	Treat "split" BAM or BED12 entries as distinct BED intervals. when computing coverage. For BAM files, this uses the CIGAR "N" and "D" operations to infer the blocks for computing coverage. For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12).
--ignore_deletion -ignoreD	boolean_true	Ignore local deletions (CIGAR "D" operations) in BAM entries when computing coverage.
--strand	string	Calculate coverage of intervals from a specific strand. With BED files, requires at least 6 columns (strand is column 6).
--pair_end_coverage -pc	boolean_true	Calculate coverage of pair-end fragments. Works for BAM files only
--fragment_size -fs	boolean_true	Force to use provided fragment size instead of read length Works for BAM files only
--du	boolean_true	Change strand af the mate read (so both reads from the same strand) useful for strand specific Works for BAM files only
--five_prime -5	boolean_true	Calculate coverage of 5" positions (instead of entire interval).
--three_prime -3	boolean_true	Calculate coverage of 3" positions (instead of entire interval).
--max	integer	Combine all positions with a depth >= max into a single bin in the histogram. Irrelevant for -d and -bedGraph - (INTEGER)
--scale	double	Scale the coverage by a constant factor. Each coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). - Default is 1.0; i.e., unscaled. - (FLOAT)
--trackline	boolean_true	Adds a UCSC/Genome-Browser track line definition in the first line of the output. - See here for more details about track line definition: http://genome.ucsc.edu/goldenPath/help/bedgraph.html - NOTE: When adding a trackline definition, the output BedGraph can be easily uploaded to the Genome Browser as a custom track, BUT CAN NOT be converted into a BigWig file (w/o removing the first line).
--trackopts	string multiple	Writes additional track line definition parameters in the first line. - Example: -trackopts 'name="My Track" visibility=2 color=255,30,30' Note the use of single-quotes if you have spaces in your parameters. - (TEXT)

Name

Type & Properties

--depth

-d

boolean_true

--depth_zero

-dz

boolean_true

--bed_graph

-bg

boolean_true

--bed_graph_zero_coverage

-bga

boolean_true

--split

boolean_true

--ignore_deletion

-ignoreD

boolean_true

--strand

string

--pair_end_coverage

-pc

boolean_true

--fragment_size

-fs

boolean_true

--du

boolean_true

--five_prime

-5

boolean_true

--three_prime

-3

boolean_true

--max

integer

--scale

double

--trackline

boolean_true

--trackopts

string

multiple

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

bedtools/bedtools_genomecov

Inputs

Outputs

Options

Run this component

Relationships

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