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Annotate somatic or germline variants output

Source: R/nextflow_annotation_utils.R
annotate_called_variants.Rd

Given a manifest, annotate data as variant data (vcf or maf).

Usage

annotate_called_variants(metadata, workflow_link, verbose = TRUE)

Arguments

metadata

Metadata table to build upon.

Workflow link to most specific part of workflow generating these data.

verbose

Give verbose reports for what's happening.

Details

maf files use the same template but with different default values. If in the future mafs require a significantly different template, then this should be factored out into a separate annotation function.