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

Source: R/statistics.R
vcf.stat.Rd

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)