Description

Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

VCF with repeat expansions

*.{vcf.gz,vcf}

meta2{:bash}

:map

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

variant_catalog{:bash}

:file

json file with repeat expansion sites to genotype

*.{json}

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

Annotated VCF file

*.{vcf.gz}

*.vcf.gz{:bash}

:map

Annotated VCF file

*.{vcf.gz}

tbi{:bash}

meta{:bash}

:map

Annotated VCF file

*.{vcf.gz}

*.vcf.gz.tbi{:bash}

:map

Index of the annotated VCF file

*.{vcf.gz.tbi}

versions_stranger{:bash}

${task.process}{:bash}

:string

The name of the process

stranger{:bash}

:string

The name of the tool

stranger --version | sed 's/stranger, version //g'{:bash}

:eval

The expression to obtain the version of the tool

versions_tabix{:bash}

${task.process}{:bash}

:string

The name of the process

tabix{:bash}

:string

The tool name

tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'{: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

stranger{:bash}

:string

The name of the tool

stranger --version | sed 's/stranger, version //g'{:bash}

:eval

The expression to obtain the version of the tool

${task.process}{:bash}

:string

The name of the process

tabix{:bash}

:string

The tool name

tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'{:bash}

:eval

The expression to obtain the version of the tool

Tools

stranger
MIT

Annotate VCF files with str variants

github.com/moonso/stranger 10.5281/zenodo.4548873
maintainer
Github user ljmesi
get in touch
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