QC of a gVCF or VCF file

Description Usage Arguments Value Examples

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.

1	ReadVCFData(mydir, myfile, genome)

`mydir`	Directory of vcf file
`myfile`	Filename of vcf file
`genome`	GRCh37 or GRCh38

Object of class VCFData

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