bedtools/bedtools_genomecov

genome coverage

BED

GFF

VCF

BAM

Description

Compute the coverage of a feature file among a genome.

Inputs

Name	Type & Properties	Description
--input -i	file	The input file (BED/GFF/VCF) to be used.
--input_bam -ibam	file	The input file is in BAM format. Note: BAM _must_ be sorted by positions. '--genome' option is ignored if you use '--input_bam' option!
--genome -g	file	The genome file to be used.

Name

Type & Properties

--input

-i

file

--input_bam

-ibam

file

--genome

-g

file

Outputs

Name	Type & Properties	Description
--output	file required output	The output BED file.

Name

Type & Properties

--output

file

required

output

Options

Name	Type & Properties	Description
--depth -d	boolean_true	Report the depth at each genome position (with one-based coordinates). Default behavior is to report a histogram.
--depth_zero -dz	boolean_true	Report the depth at each genome position (with zero-based coordinates). Reports only non-zero positions. Default behavior is to report a histogram.
--bed_graph -bg	boolean_true	Report depth in BedGraph format. For details, see: genome.ucsc.edu/goldenPath/help/bedgraph.html
--bed_graph_zero_coverage -bga	boolean_true	Report depth in BedGraph format, as above (-bg). However with this option, regions with zero coverage are also reported. This allows one to quickly extract all regions of a genome with 0 coverage by applying: "grep -w 0$" to the output.
--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.bed"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/bedtools/bedtools_genomecov/main.nf \  
  -params-file params.yaml

bedtools/bedtools_genomecov

Inputs

Outputs

Options

Run this component

Relationships

Used by

Uses