annotateVcf: Annotate a VCF file

In seqminer: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

Annotate a VCF file

Description

Annotate a VCF file

Usage

annotateVcf(inVcf, outVcf, params)

Arguments

inVcf	input VCF file name
outVcf	output VCF file name
params	parameters

Value

0 if succeed

Examples

param <- list(reference = system.file("tabanno/test.fa", package = "seqminer"),
              geneFile = system.file("tabanno/test.gene.txt", package = "seqminer"))
param <- makeAnnotationParameter(param)
inVcf <- system.file("tabanno/input.test.vcf", package = "seqminer")
outVcf <- file.path(tempdir(), "/", "out.vcf")
annotateVcf (inVcf, outVcf, param)
cat('Annotated VCF files are in the temp directory:', outVcf, '\n')

seqminer documentation built on Sept. 2, 2023, 9:08 a.m.