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{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

stranger
MIT

Annotate VCF files with str variants

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