Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

]

vcf (file)

VCF with repeat expansions

*.{vcf.gz,vcf}

meta2 (map)

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

variant_catalog (file)

json file with repeat expansion sites to genotype

*.{json}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

vcf (file)

annotated VCF with keys STR_STATUS, NormalMax and PathologicMin

*.{vcf.gz}
included in
raredisease
maintainer
Github user ljmesi
get in touch
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Tools

stranger
MIT

Annotate VCF files with str variants

github.com/moonso/stranger 10.5281/zenodo.4548873