vcfToMAF: vcfToMAF

View source: R/vcfToMAF.R

vcfToMAFR Documentation

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.