Get Sarek VCF output files for a SCOUT SPN — get_sarek_vcf • SCOUT

Returns a named list of VCF (and index) file paths from the Sarek variant calling results for a given sample, coverage, purity and caller.

Usage

get_sarek_vcf(
  spn,
  sample_id,
  coverage,
  purity,
  caller,
  type,
  normal_id = "normal_sample"
)

Arguments

spn: SPN identifier, e.g. "SPN01".
sample_id: Sample identifier.
coverage: Sequencing coverage (integer, e.g. 100).
purity: Sample purity (0–1, e.g. 0.9).
caller: VCF caller: "mutect2", "strelka", "freebayes", or "haplotypecaller".
type: Sample type: "tumour" or "normal".
normal_id: Normal sample ID. Defaults to "normal_sample".

Value

Named list of file paths (keys depend on caller, e.g. vcf, tbi, snvs_vcf, etc.).

Examples

if (FALSE) { # \dontrun{
get_sarek_vcf("SPN01", "SPN01_1", 100, 0.9, "mutect2", "tumour")
} # }