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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