mutFilterPON: mutFilterPON

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

mutFilterPON

Description

Filter variants based on Panel of Normals

Usage

mutFilterPON(maf, PONfile, PONformat = "vcf", 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"
verbose	Whether to generate message/notification during the filtration process. Default: TRUE.

Value

An MAF data frame where some variants have P tag in CaTag column for PON filtration.

Examples

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

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