mutFilterDB: mutFilterDB

In likelet/CaMutQC: An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations

mutFilterDB

Description

Filter variants in germline database.

Usage

mutFilterDB(
  maf,
  dbVAF = 0.01,
  ExAC = TRUE,
  Genomesprojects1000 = TRUE,
  ESP6500 = TRUE,
  gnomAD = TRUE,
  dbSNP = FALSE,
  keepCOSMIC = TRUE,
  verbose = TRUE
)

Arguments

maf	An MAF data frame, generated by vcfToMAF function.
dbVAF	Threshold of VAF value for database annotations. Default: 0.01.
ExAC	Whether to filter variants listed in ExAC with VAF higher than cutoff (set in dbVAF parameter). Default: TRUE.
Genomesprojects1000	Whether to filter variants listed in Genomesprojects1000 with VAF higher than cutoff (set in dbVAF parameter). Default: TRUE.
ESP6500	Whether to filter variants listed in ESP6500 with VAF higher than cutoff (set in dbVAF parameter). Default: TRUE.
gnomAD	Whether to filter variants listed in gnomAD with VAF higher than cutoff (set in dbVAF parameter). Default: TRUE.
dbSNP	Whether to filter variants listed in dbSNP. Default: FALSE.
keepCOSMIC	Whether to keep variants in COSMIC even they are present in germline database. Default: TRUE.
verbose	Whether to generate message/notification during the filtration process. Default: TRUE.

Value

An MAF data frame after filtration for database and clinical significance

Examples

maf <- vcfToMAF(system.file("extdata",
"WES_EA_T_1_mutect2.vep.vcf", package="CaMutQC"))
mafF <- mutFilterDB(maf)

likelet/CaMutQC documentation built on Aug. 17, 2024, 4 a.m.