GetVAF: Extract the VAFs (variant allele frequencies) and read depth...

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

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)

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.

Value

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

Note

GetPCAWGConsensusVAF is analogous to GetMutectVAF, calculating VAF and read depth from PCAWG7 consensus vcfs

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)

ICAMS documentation built on June 15, 2025, 1:08 a.m.