Description

Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

intervals1 (file)

BED/GFF/VCF

*.{bed|gff|vcf}

intervals2 (file)

BED/GFF/VCF

*.{bed|gff|vcf}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

bed (file)

File containing the difference between the two sets of features

versions (file)

File containing software versions

versions.yml
author
Github user sidorov-si
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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/subtract