Description

Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bed (file)

Input BED file

*.{bed}

sizes (file)

File which defines the chromosome lengths for a given genome

*.{sizes}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

bed (file)

Bed file with all genomic intervals that are not covered by at least one record from the input file.

*.{bed}

versions (file)

File containing software versions

versions.yml
included in
cutandrun
authors
Github user Emiller88 Github user sruthipsuresh Github user drpatelh
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/complement