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Function that performs a sanity check of query VCF for pcgrr package, ensuring that all required tags are present in annotated VCF

Usage

data_integrity_check(vcf_df, pcgr_data, config = NULL, workflow = "pcgr")

Arguments

vcf_df

data frame with variants from VCF

pcgr_data

PCGR data object

config

PCGR/CPSR config object

workflow

type of workflow (pcgr/cpsr)