Function that sets STATUS_POPFREQ_1KG_ABOVE_TOLERATED/ STATUS_POPFREQ_GNOMAD_ABOVE_TOLERATED to TRUE for variants if any population frequency exceeds max_tolerated_af — assign_germline_popfreq_status • PCGR

Function that sets STATUS_POPFREQ_1KG_ABOVE_TOLERATED/ STATUS_POPFREQ_GNOMAD_ABOVE_TOLERATED to TRUE for variants if any population frequency exceeds max_tolerated_af

Usage

assign_germline_popfreq_status(
  sample_calls,
  pop = "EUR",
  dbquery = "1KG",
  max_tolerated_af = 0.01
)

Arguments

sample_calls: data frame with variants
pop: population code (1000 Genomes/gnomAD)
dbquery: 1KG or gnomAD
max_tolerated_af: max tolerated germline allele frequency

Value

sample_calls