vcfToDNVcatalogue: VCF to DNV catalogue

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

VCF to DNV catalogue

Description

Convert a vcf file containing SNVs and DNVs to a DNV catalogue. The VCF file should containt the SNVs and/or DNVs of a single sample. Two SNVs that are next to each other will be combined into a DNV.

Usage

vcfToDNVcatalogue(vcfFilename, genome.v = "hg19")

Arguments

vcfFilename	path to input VCF (file must be tabix indexed)
genome.v	either "hg38" (will load BSgenome.Hsapiens.UCSC.hg38), "hg19" (will load BSgenome.Hsapiens.1000genomes.hs37d5), mm10 (will load BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10) or canFam3 (will load BSgenome.Cfamiliaris.UCSC.canFam3::BSgenome.Cfamiliaris.UCSC.canFam3)

Value

returns the DNV catalogue for the given sample and mutation list

Examples

file_muts <- "mutations.vcf"
res <- vcfToSNVcatalogue(file_muts,genome.v = "hg38")

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.