modules/vcfanno

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

vcfbedannotatevariantluatoml

https://github.com/nf-core/modules/[...]/modules/nf-core/vcfanno

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:false ]

`vcf:file`

query VCF file

*.{vcf, vcf.gz}

`tbi:file`

tabix index file for the query VCF

*.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

`vcf`

`meta:map`

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

`*.vcf:file`

Annotated VCF file

*.vcf

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

github.com/brentp/vcfanno#vcfanno https://github.com/brentp/vcfanno 10.1186/s13059-016-0973-5

modules/vcfanno

Description

Input

`meta:map`

`vcf:file`

`tbi:file`

`specific_resources:map`

`toml:file`

`lua:file`

`resources:map`

Output

`vcf`

`meta:map`

`*.vcf:file`

`versions`

`versions.yml:file`

Tools

vcfanno

included in

maintainers

get in touch