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:false ]

bed:file

Input BED file

*.{bed}

sizes:file

File which defines the chromosome lengths for a given genome

*.{sizes}

Output

name:type
description
pattern

bed

meta:map

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

*.bed:file

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

*.{bed}

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/complement
included in
cutandruntfactivity
maintainers
Github user edmundmiller
Github user sruthipsuresh
Github user drpatelh
get in touch
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