Get sequencing quality statistics of raw VCF files (with GatK generated vcf files only)

This function will generate a table similar to VariantsToTable option in GatK from raw vcf files for filtering purposes. The function will also plot all the parameters (see details & values).

Usage

vcf.stat(vcf, plot = TRUE, ...)

Arguments

vcf: an imported vcf file in data.frame or matrix format using readVCF
plot: logical. Whether to plot the (12) parameters
...: other arguments passed on to plot (e.g. col,border)

Value

Returns a data frame with quality parameters from the INFO. field of the vcf

QUAL: The Phred-scaled probability that a REF/ALT polymorphism exists at this site given sequencing data
AC: Allele count
AF: Allele frequency
DP: unfiltered depth
QD: QualByDepth - This is the variant confidence (from the QUAL field) divided by the unfiltered depth of non-hom-ref samples
FS: FisherStrand - This is the Phred scaled probability that there is strand bias at the site
SOR: StrandOddsRatio - This is another way to estimate strand bias using a test similar to the symmetric odds ratio test
MQ: RMSMappingQuality - This is the root mean square mapping quality over all the reads at the site
MQRankSum: MappingQualityRankSumTest - This is the u-based z-approximation from the Rank Sum Test for mapping qualities
ReadPosRankSum: ReadPosRankSumTest: This is the u-based z-approximation from the Rank Sum Test for site position within reads

Details

For more details see instructions of GatK

Author

Piyal Karunarathne

Examples

vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path=vcf.file.path)
statistics<-vcf.stat(vcf,plot=TRUE)