ICAMS (version 3.0.11)

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)
GetPCAWGConsensusVAF(vcf, mc.cores = 1)

Value

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

Arguments

vcf

An in-memory VCF data frame.

name.of.VCF

Name of the VCF file.

tumor.col.name

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

mc.cores

The number of cores to use. Not available on Windows unless mc.cores = 1.

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)