vcfToMAF: vcfToMAF

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

vcfToMAF

Description

Format transformation from VCF to MAF.

Usage

vcfToMAF(
  vcfFile,
  multiVCF = FALSE,
  inputStrelka = FALSE,
  writeFile = FALSE,
  MAFfile = "MAF.maf",
  MAFdir = "./",
  tumorSampleName = "Extracted",
  normalSampleName = "Extracted",
  ncbiBuild = "Extracted",
  MAFcenter = ".",
  MAFstrand = "+",
  filterGene = FALSE,
  simplified = FALSE
)

Arguments

vcfFile	Directory of a VCF file, or the path to several VCF files that is going to be transformed. Files should be in .vcf or .vcf.gz format.
multiVCF	Logical, whether the input is a path that leads to several VCFs that come from multi-region/sample/caller sequencing. Default: FALSE
inputStrelka	The type of variants ('INDEL' or 'SNV') in VCF file if it is from Strelka. Default: FALSE
writeFile	Whether to directly write MAF file to the disk. If FALSE, a MAF data frame will be returned. If TRUE, a MAF file will be saved. Default: FALSE.
MAFfile	File name of the exported MAF file, if writeFile is set as TRUE.
MAFdir	Directory of the exported MAF file, if writeFile is set as TRUE.
tumorSampleName	Name of the tumor sample(s) in the VCF file(s). If it is set as 'Extracted', tumorSampleName would be extracted automatically from the VCF file. Default: 'Extracted'.
normalSampleName	Name the normal sample in the VCF file. If it is set as 'Extracted', normalSampleName would be extracted automatically from the VCF file. Default: 'Extracted'.
ncbiBuild	The reference genome used for the alignment, which will be presented as value in 'NCBIbuild' column in MAF file. Default: 'GRCh38'.
MAFcenter	One or more genome sequencing center reporting the variant, which will be presented as value in 'Center' column in MAF. Default: '.'.
MAFstrand	Genomic strand of the reported allele, which will be presented as value in 'Strand' column in MAF file. Default: '+'.
filterGene	Logical. Whether to filter variants without Hugo Symbol. Default: FALSE
simplified	Logical. Whether to extract the first thirteen columns after converting to MAF file. Default: FALSE

Value

A detailed MAF data frame

Examples

maf <- vcfToMAF(system.file("extdata", "WES_EA_T_1_mutect2.vep.vcf",
package="CaMutQC"))

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