ICAMS (version 2.3.12)

GetVAF: Extract the VAFs (variant allele frequencies) and read depth information from a VCF file

Description

Extract the VAFs (variant allele frequencies) and read depth information from a VCF file

Usage

GetStrelkaVAF(vcf, name.of.VCF = NULL)
GetMutectVAF(vcf, name.of.VCF = NULL, tumor.col.name = NA)
GetFreebayesVAF(vcf, name.of.VCF = NULL)

Value

The original vcf with two additional columns added which contain the VAF(variant allele frequency) and read depth information.

Arguments

vcf

Said VCF as a data.frame.

name.of.VCF

Name of the VCF file.

tumor.col.name

Optional. Only applicable to Mutect VCF. Name of the column in Mutect VCF which contains the tumor sample information. It must have quotation marks. If tumor.col.name is equal to NA(default), this function will use the 10th column to calculate VAFs.

Examples

file <- c(system.file("extdata/Strelka-SBS-vcf",
                      "Strelka.SBS.GRCh37.s1.vcf",
                      package = "ICAMS"))
MakeDataFrameFromVCF <- getFromNamespace("MakeDataFrameFromVCF", "ICAMS")
df <- MakeDataFrameFromVCF(file)
df1 <- GetStrelkaVAF(df)