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

]

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.

Output

Name (Type)
Description
Pattern

meta (map)

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

]

genomecov (file)

Computed genome coverage file

*.${extension}

versions (file)

File containing software versions

versions.yml
included in
cutandrun hicar nascent raredisease
maintainers
Github user edmundmiller
Github user sruthipsuresh
Github user drpatelh
Github user sidorov-si
Github user chris-cheshire
get in touch
Ask a question on Slack Open an issue on GitHub

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