Description

computes both the depth and breadth of coverage of features in file B on the features in file A

Input

name:type
description
pattern

meta

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

input_A

:file

BAM/BED/GFF/VCF file

*.{bam,bed,gff,vcf}

input_B

:file

One or more BAM/BED/GFF/VCF file

*.{bam,bed,gff,vcf}

genome_file

:file

Optional reference genome 2 column file that defines the expected chromosome order in the input files for use with the -sorted option. When genome_file is provided, -sorted option is added to the command.

*.{fai,txt,chromsizes}

Output

name:type
description
pattern

bed

meta

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.bed

:file

File containing coverage of sequence alignments

*.bed

versions_bedtools

${task.process}

:string

The name of the process

bedtools

:string

The name of the tool

bedtools --version | sed -e 's/bedtools v//g'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

bedtools

:string

The name of the tool

bedtools --version | sed -e 's/bedtools v//g'

:eval

The expression to obtain the version of the tool

Tools

included in
radseq
maintainer
Github user priyanka-surana
get in touch
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