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Get Sarek VCF output files for a SCOUT SPN

get_sarek_vcf.Rd

Returns a named list of VCF (and index) file paths from the Sarek variant calling results for a given sample, coverage, purity and caller. Supported callers: "mutect2", "strelka", "freebayes", "haplotypecaller".

Usage

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

Arguments

spn

SPN identifier, e.g. "SPN04".

sample

Sample identifier, e.g. "SPN04_1.1". Not required for "mutect2" (SPN-level) or normal-only callers.

coverage

Sequencing coverage (integer, e.g. 100).

purity

Sample purity: 0.9, 0.6, or 0.3.

caller

VCF caller: "mutect2", "strelka", "freebayes", or "haplotypecaller".

normal_id

Normal sample ID. Defaults to "normal_sample".

Value

Named list of file paths.

Examples

if (FALSE) { # \dontrun{
get_sarek_vcf("SPN04", "SPN04_1.1", 100, 0.3, "mutect2")
get_sarek_vcf("SPN04", "SPN04_1.1", 100, 0.3, "strelka")
get_sarek_vcf("SPN04", NULL, 100, 0.3, "haplotypecaller")
} # }