Function that reads CPSR-classified variants from a TSV file

Usage

load_cpsr_classified_variants(
  fname_cpsr_tsv = NA,
  fname_cpsr_yaml = NA,
  cols = NULL,
  ignore_vus = FALSE,
  ref_data = NULL,
  settings = NULL
)

Arguments

fname_cpsr_tsv: Path to raw input file with CPSR-classified SNVs/InDels
fname_cpsr_yaml: Path to YAML configuration file for CPSR analysis
cols: column type definitions of raw input file
ignore_vus: logical indicating if VUS should be ignored in report
ref_data: PCGR reference data object
settings: PCGR run/configuration settings