Description

bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing interval information e.g. [ id:‘test’ ]

intervals{:bash}

:file

Input interval (BED/GFF/VCF) file

*.{bed,gff,gff3,vcf}

meta2{:bash}

:map

Groovy Map containing genome information e.g. [ id:‘test’ ]

chrom_sizes{:bash}

:file

Chromosome sizes file

*{.genome,.sizes,.txt,.fai}

exclude_file{:bash}

:file

BED file containing regions to exclude

*.{bed}

include_file{:bash}

:file

BED file containing regions to include

*.{bed}

Output

name:type
description
pattern

bed{:bash}

meta{:bash}

:map

Groovy Map containing interval information e.g. [ id:'sample1' ]

*.bed{:bash}

:file

BED file with shuffled intervals

*.{bed}

versions_bedtools{:bash}

${task.process}{:bash}

:string

The name of the process

bedtools{:bash}

:string

The name of the tool

bedtools --version | sed -e 's/bedtools v//g'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

bedtools{:bash}

:string

The name of the tool

bedtools --version | sed -e 's/bedtools v//g'{:bash}

:eval

The expression to obtain the version of the tool

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/slop
included in
deepmodeloptim
maintainer
Github user itrujnara
get in touch
Ask a question on Slack Open an issue on GitHub