Description

quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files

Input

Name (Type)
Description
Pattern

meta (map)

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

]

vcf (file)

query VCF file

*.{vcf, vcf.gz}

vcf_tabix (file)

tabix index of query VCF - only needed if vcf is compressed

*.vcf.gz.tbi

specific_resources (map)

A list of sample specific reference files defined in toml config, must also include indices if bgzipped.

toml (file)

configuration file with reference file basenames

*.toml

lua (file)

Lua file for custom annotations

*.lua

resources (map)

List of reference files defined in toml config, must also include indices if bgzipped.

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 file

*.vcf
included in
raredisease
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