Description

Call variants for a given scenario specified with the varlociraptor calling grammar, preprocessed by varlociraptor preprocessing

Input

name:type
description
pattern

meta{:bash}

:map

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

vcfs{:bash}

:file

Sorted VCF/BCF file containing sample observations, Can also be a list of files

*.{vcf,bcf,vcf.gz}

scenario{:bash}

:file

Yaml file containing scenario information (optional)

*.{yml,yaml}

scenario_aliases{:bash}

:list

List of aliases for the scenario (optional)

Output

name:type
description
pattern

bcf{:bash}

meta{:bash}

:map

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

*.bcf{:bash}

:file

BCF file containing sample observations

*.bcf

versions_varlociraptor{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

varlociraptor{:bash}

:string

The tool name

varlociraptor --version | sed 's/^varlociraptor //'{:bash}

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

varlociraptor{:bash}

:string

The tool name

varlociraptor --version | sed 's/^varlociraptor //'{:bash}

:string

The command used to generate the version of the tool

Tools

varlociraptor
GPL v3

Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.

varlociraptor.github.io/docs/estimating varlociraptor.github.io/docs/calling https://github.com/varlociraptor/varlociraptor 10.1186/s13059-020-01993-6
included in
sarek
maintainers
Github user FriederikeHanssen
Github user famosab
get in touch
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