Description

Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.

Input

name:type
description
pattern

meta:map

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

intervals:file

BAM/BED/GFF/VCF

*.{bam|bed|gff|vcf}

scale:integer

Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch

sizes:file

Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column

extension:string

Extension of the output file (e. g., “.bg”, “.bedgraph”, “.txt”, “.tab”, etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.

sort:boolean

Sort the output

Output

name:type
description
pattern

genomecov

meta:map

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

*.${extension}:file

Computed genome coverage file

*.${extension}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

bedtools
MIT

A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.

bedtools.readthedocs.io/en/latest/content/tools/genomecov
included in
cutandrunhicarnascentrarediseasernaseq
maintainers
Github user edmundmiller
Github user sruthipsuresh
Github user drpatelh
Github user sidorov-si
Github user chris-cheshire
get in touch
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