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

versions.yml:file

File containing software versions

versions.yml

Tools

included in
radseq
maintainer
Github user priyanka-surana
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