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

*.{bam|bed|gff|vcf}

intervals2 (file)

BAM/BED/GFF/VCF

*.{bam|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

]

intersect (file)

File containing the description of overlaps found between the two features

*.${extension}

versions (file)

File containing software versions

versions.yml
included in
cutandrun nascent radseq
authors
Github user Emiller88 Github user sruthipsuresh Github user drpatelh Github user sidorov-si
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/intersect.html