QC of a gVCF or VCF file

Description Usage Arguments Value Examples

Getter for VCFQAReport class to return results. Return a list showing values that the sample was evaluated on.

1	getResults(Object)

Object

an object of type VCFQAReport

numeric vector of results

vcffn <- system.file("ext-data", "chr22.GRCh38.vcf.gz", package="genotypeeval")
mydir <- paste(dirname(vcffn), "/", sep="")
myfile <-basename(vcffn)
svp <- ScanVcfParam(which=GRanges("22", IRanges(0,200e5)), geno="GT")
vcfparams <- VCFQAParam(count.limits=c(3014580000, Inf), readdepth.target = 30)
vcf <- ReadVCFData(mydir, myfile, "GRCh38")
ev <- VCFEvaluate(vcf, vcfparams)
getResults(ev)