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Function that reads and validates an annotated somatic SNV/InDel file from PCGR pre-reporting pipeline

Source: R/input_data.R
load_somatic_snv_indel.Rd

Function that reads and validates an annotated somatic SNV/InDel file from PCGR pre-reporting pipeline

Usage

load_somatic_snv_indel(
  fname = NA,
  ref_data = NULL,
  settings = NULL,
  simulate_vaf_dp = FALSE
)

Arguments

fname

Path to file with pre-processed somatic SNV/InDel variants

ref_data

PCGR reference data object

settings

PCGR run/configuration settings

simulate_vaf_dp

Internal/test use only. If TRUE and VAF_TUMOR is entirely missing, replace it with random values drawn from Uniform(0.01, 0.99). Never set this in production runs.