Description

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

Input

name:type
description
pattern

meta:map

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

normal_vcf:file

Sorted VCF/BCF file (list)

*.{bcf,vcf,vcf.gz}

tumor_vcf:file

Sorted VCF/BCF file (optional)

*.{bcf,bcf.gz,vcf,vcf.gz}

scenario:file

Yaml file containing scenario information (optional)

*.{yml,yaml}

scenario_sample_name:string

Sample name for the scenario

Output

name:type
description
pattern

bcf_gz

meta:map

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

*.bcf.gz:file

BCF file containing sample observations

*.bcf.gz

vcf_gz

meta:map

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

*.vcf.gz:file

Compressed VCF file containing sample observations

*.vcf.gz

bcf

meta:map

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

*.bcf:file

BCF file containing sample observations

*.bcf

vcf

meta:map

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

*.vcf:file

VCF file containing sample observations

*.vcf

versions

versions.yml:file

File containing software versions

versions.yml

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
Github user FriederikeHanssen
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