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{:bash}

:map

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

vcf{:bash}

:file

query VCF file

*.{vcf, vcf.gz}

tbi{:bash}

:file

tabix index file for the query VCF

*.tbi

specific_resources{:bash}

:map

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

toml{:bash}

:file

configuration file with reference file basenames

*.toml

lua{:bash}

:file

Lua file for custom annotations

*.lua

resources{:bash}

:map

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

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz

*.vcf.gz{:bash}

:map

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

*.vcf.gz

tbi{:bash}

meta{:bash}

:map

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

*.vcf.gz

*.vcf.gz.tbi{:bash}

:map

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

*.vcf.gz.tbi

versions_vcfanno{:bash}

${task.process}{:bash}

:string

The name of the process

vcfanno{:bash}

:string

The name of the tool

vcfanno 2>&1 | sed -n 's/.*version \([0-9.]\+\).*/\1/p'{: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

vcfanno{:bash}

:string

The name of the tool

vcfanno 2>&1 | sed -n 's/.*version \([0-9.]\+\).*/\1/p'{:bash}

:eval

The expression to obtain the version of the tool

Tools

included in
raredisease
maintainers
Github user projectoriented
Github user matthdsm
Github user nvnieuwk
get in touch
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