mutFilterQual: mutFilterQual

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

mutFilterQual

Description

Filter variants in low sequencing quality or low confidence.

Usage

mutFilterQual(
  maf,
  panel = "Customized",
  tumorDP = 20,
  normalDP = 10,
  tumorAD = 5,
  normalAD = Inf,
  VAF = 0.05,
  VAFratio = 0
)

Arguments

maf	An MAF data frame, generated by vcfToMAF function.
panel	The sequencing panel applied on the dataset. Parameters for mutFilterQual function are set differently for different panels. Default: "Customized". Options: "MSKCC", "WES".
tumorDP	Threshold of tumor total depth. Default: 20
normalDP	Threshold of normal total depth. Default: 10
tumorAD	Threshold of tumor alternative allele depth. Default: 5
normalAD	Threshold of normal alternative allele depth. Default: Inf
VAF	Threshold of VAF value. Default: 0.05
VAFratio	Threshold of VAF ratio (tVAF/nVAF). Default: 0

Value

An MAF data frame where some variants have Q tag in CaTag column for sequencing quality filtration

Examples

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

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