Function that reads and validates CNA or SNV/InDel TSV files file from PCGR/CPSR pre-report (Python) pipeline

Usage

load_dna_variants(
  fname = NA,
  cols = NULL,
  ref_data = NULL,
  vartype = "snv_indel",
  primary_site = "Any",
  retained_info_tags = "None",
  variant_origin = "Somatic"
)

Arguments

fname: Path to raw input file with DNA aberrations (PCGR/CPSR)
cols: column type definitions of raw input file
ref_data: PCGR reference data object
vartype: type of DNA aberrations ('snv_indel','cna')
primary_site: primary site of tumor
retained_info_tags: VCF INFO tags to be retained in output (SNVs/InDels)
variant_origin: Germline/Somatic