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

]

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 (string)

(List of) sample name(s) to be processed as named in the scenario yml (optional)

*.{bcf,vcf,vcf.gz}

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_gz (file)

Compressed VCF file containing sample observations

*.vcf.gz

bcf_gz (file)

BCF file containing sample observations

*.bcf.gz

vcf (file)

VCF file containing sample observations

*.vcf

bcf (file)

BCF file containing sample observations

*.bcf
author
Github user FriederikeHanssen
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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