Annotate somatic or germline variants output
Source:R/nextflow_annotation_utils.R
annotate_called_variants.RdCurrently, vcf are output first and mafs appear after a subsequent workflow run,
so depending on when map_sample_output_sarek is run to create a sample_io file,
there will be just vcf files or both.
(In the future, the workflows will likely be joined so both are deposited at the same run.)
One can specify to only annotate either the "vcf" or "maf" files and create a manifest
for just those files, or use "auto" to detect the file types present in sample_io.
Usage
annotate_called_variants(
sample_io,
workflow_ref,
format = c("auto", "vcf", "maf"),
template = "bts:ProcessedVariantCallsTemplate",
schema =
"https://raw.githubusercontent.com/nf-osi/nf-metadata-dictionary/main/NF.jsonld",
data_type = c("auto", "SomaticVariants", "GermlineVariants",
"AnnotatedSomaticVariants", "AnnotatedGermlineVariants"),
verbose = TRUE,
dry_run = TRUE
)Arguments
- sample_io
Table mapping input to outputs, which reference output
.vcf.gzormaffiles.- workflow_ref
Character vector with names for workflow and values as version-specific links.
- format
Variant format, "auto" to handle any "vcf" or "maf" files present automatically, or specify one explicitly. See details.
- template
(Optional) URI of template in data model to use, prefixed if needed. Can specify different model/version, but in some cases may not work well.
- schema
Path (URL or local) to file from which schema will be read, or schema as list object.
- data_type
Variant type, use "auto" to infer from naming scheme and current NF processing SOP, or specify more explicitly.
- verbose
Give verbose reports for what's happening.
- dry_run
Whether to apply annotations.