Function that generates tiered variant sets for SNVs/InDels — generate_report_data_snv_indel • PCGR

Function that generates tiered variant sets for SNVs/InDels

Usage

generate_report_data_snv_indel(
  sample_calls,
  pcgr_data,
  sample_name,
  config,
  callset = "somatic calls",
  biomarker_mapping_stringency = 1,
  tier_model = "pcgr_acmg"
)

Arguments

sample_calls: variant calls subject to mutational signature analysis
pcgr_data: object with PCGR annotation data
sample_name: sample identifier
config: Object with PCGR configuration parameters
callset: type of calls
biomarker_mapping_stringency: quality level for biomarkers
tier_model: tier model (pcgr_acmg)

Value

pcg_report_data data frame with all report elements