Description

Writes an interval list created by splitting a reference at Ns.A Program for breaking up a reference into intervals of alternating regions of N and ACGT bases

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

Fasta file to derive the intervals from

*.{fasta,fa,fna}

meta2{:bash}

:map

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

fai{:bash}

:file

Index of the fasta file

*.fai

meta3{:bash}

:map

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

dict{:bash}

:file

Sequence dictionary of the fasta file

*.dict

Output

name:type
description
pattern

intervals{:bash}

meta{:bash}

:map

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

*.interval_list{:bash}

:file

The scattered intervals

*.interval_list

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

picard
MIT

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

broadinstitute.github.io/picard https://github.com/broadinstitute/picard
maintainer
Github user nvnieuwk
get in touch
Ask a question on Slack Open an issue on GitHub