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

]

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

meta (map)

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

]

bed (file)

File containing coverage of sequence alignments

*.bed

versions (file)

File containing software versions

versions.yml
included in
radseq
maintainer
Github user priyanka-surana
get in touch
Ask a question on Slack Open an issue on GitHub

Tools