Description

Allows one to screen for overlaps between two sets of genomic features.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

intervals1 (file)

BAM/BED/GFF/VCF

*.{bed|gff|vcf}

intervals2 (file)

BAM/BED/GFF/VCF

*.{bed|gff|vcf}

meta2 (map)

Groovy Map containing reference chromosome sizes
e.g. [ id:‘test’ ]

chrom_sizes (file)

Chromosome sizes file

*{.sizes,.txt}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

mapped (file)

File containing the description of overlaps found between the features in A and the features in B, with statistics

*.${extension}

versions (file)

File containing software versions

versions.yml
maintainer
Github user ekushele
get in touch
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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/map