mutFilterTech: mutFilterTech

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

mutFilterTech

Description

Filter potential artifacts produced through technical issue, including filtration for sequencing quality, strand bias, adjacent indel tag, normal depth, panel of normal (PON) and FILTER field.

Usage

mutFilterTech(
  maf,
  PONfile,
  PONformat = "vcf",
  panel = "Customized",
  tumorDP = 20,
  normalDP = 10,
  tumorAD = 5,
  normalAD = Inf,
  VAF = 0.05,
  VAFratio = 0,
  SBmethod = "SOR",
  SBscore = 3,
  maxIndelLen = 50,
  minInterval = 10,
  tagFILTER = "PASS",
  progressbar = TRUE,
  verbose = TRUE
)

Arguments

maf	An MAF data frame, generated by vcfToMAF function.
PONfile	Panel-of-Normals files, which can be either obtained through GATK (https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON-) or generated by users. Should have at least four columns: CHROM, POS, REF, ALT
PONformat	The format of PON file, either "vcf" or "txt". Default: "vcf"
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
SBmethod	Method will be used to detect strand bias, including 'SOR' and 'Fisher'. Default: 'SOR'. SOR: StrandOddsRatio (https://gatk.broadinstitute.org/hc/en-us/articles/360041849111- StrandOddsRatio)
SBscore	Cutoff strand bias score used to filter variants. Default: 3
maxIndelLen	Maximum length of indel accepted to be included. Default: 50
minInterval	Minimum length of interval between an SNV and an indel accepted to be included. Default: 10
tagFILTER	Variants with specific tag in FILTER column will be kept, set to NULL if you want to skip this filter. Default: 'PASS'
progressbar	Whether to show progress bar when running this function Default: TRUE
verbose	Whether to generate message/notification during the filtration process. Default: TRUE.

Value

An MAF data frame after filtration for technical issue

Examples

maf <- vcfToMAF(system.file("extdata",
"WES_EA_T_1_mutect2.vep.vcf", package="CaMutQC"))
mafF <- mutFilterTech(maf, PONfile=system.file("extdata",
"PON_test.txt", package="CaMutQC"), PONformat="txt")

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