genotypeeval (version 1.2.2)

ReadVCFData: User Constructor for class. Calls VCFData constructor: ReadVCFData is a wrapper for readVcfAsVRanges. It removes indels, GL chromosomes, and MULTI calls. It scans the header of the vcf file and adds in the following fields for analysis if present: AD, GT, DP, GQ. Looks for the "END" tag in the header and reads in file as gVCF if necessary.

Description

User Constructor for class. Calls VCFData constructor: ReadVCFData is a wrapper for readVcfAsVRanges. It removes indels, GL chromosomes, and MULTI calls. It scans the header of the vcf file and adds in the following fields for analysis if present: AD, GT, DP, GQ. Looks for the "END" tag in the header and reads in file as gVCF if necessary.

Usage

ReadVCFData(mydir, myfile, genome)

Arguments

mydir

Directory of vcf file

myfile

Filename of vcf file

genome

GRCh37 or GRCh38

Value

• Object of class VCFData

Examples

vcffn <- system.file("ext-data", "chr22.GRCh38.vcf.gz", package="genotypeeval")
mydir <- paste(dirname(vcffn), "/", sep="")
myfile <-basename(vcffn)
vcf <- ReadVCFData(mydir, myfile, "GRCh38")