Function that reads a fully annotated VCF from PCGR VEP/vcfanno pipeline — get_calls • PCGR

Function that reads a fully annotated VCF from PCGR VEP/vcfanno pipeline

Usage

get_calls(
  tsv_gz_file,
  pcgr_data,
  sample_name,
  config,
  oncotree = NULL,
  cpsr = F,
  n_lines_skip = 1,
  maf_filenames = NULL
)

Arguments

tsv_gz_file: Bgzipped VCF file
pcgr_data: object with PCGR annotation data
sample_name: sample identifier
config: Object with PCGR configuration parameters
oncotree: data frame with sample-dependent phenotype terms from UMLS
cpsr: logical indicating call retrieval from CPSR workflow
n_lines_skip: number of lines to skip from vcf2tsv file
maf_filenames: list with filenames for sample MAFs (temp and final)

Value

vcf_data_df