Man pages for genotypeeval
QA/QC of a gVCF or VCF file

admixtureadmixture - estimate admixture components using supervised...
callbyChrPlotDot plot of variant call counts (hom alt and het) by...
calltypePlotBar plot of variants (counts)
chunkDatachunkData is a private function to read in a chunk and...
computeTiTvPrivate function to calc transition tranversion (titv) ratio
didSamplePassGetter for VCFEvaluate class to check if Sample Passed....
didSamplePassOverallGetter for VCFEvaluate class to check if Sample Passed....
genotypeQualityPlotHistogram of genotype qualities
getCoefsPrivate function to calc coefficients for admixture
getNameGetter for VCFQAReport class to return filename slot
getPlotsGetter for VCFQAReport class to return plots slot.
getResultsGetter for VCFQAReport class to return results. Return a...
getVRgetVr is a Getter. Returns vr slot.
goldCompareComparator to gold standard
GoldData-classDeclare class Gold to store information from Gold" (1000...
GoldDataFromGRangesUser Constructor for class. Used to associate the gold...
GoldDataParamUser Constructor for class
GoldDataParam-classDeclare class GoldDataParam which will store thresholds to...
hetGapGap between HETs by Chromosome
hetsMaskedNumber hets in masked GRanges
homrefPlotDot plot of variant call counts (hom ref) by chromosome
meanGQMean Genotype Quality (GQ)
myfPrivate function to calc likelihood for admixture
numberCallsTotal Calls. This is the total number of calls in the file...
numberOfHetsCount Number of Hets
numberOfHomRefsCount Number of Hom Ref
numberOfHomVarsCount Number of Hom Vars
percentHetsPercent of Hets as Total number of variants
percentInTargetpercent in target range read depth For 15 to 60 for 30x (50...
rareCompareComparator to rare variants. Rare is defined as 0.01 percent...
readDepthMedian read depth
readdepthPlotHistogram of read depth by GT
ReadGoldDataUser Constructor for class
ReadVCFDataUser Constructor for class. Calls VCFData constructor:...
ReadVCFDataChunkUser Constructor for class. Calls VCFData constructor:...
readVcfGoldPrivate method for class. Read in Gold file - will read in...
reformatDataTake in the results from the population data and re-format it
titvTransition transversion ratio in coding and non-coding
VCFData-classDeclare class Reads in VCF using readVCFAsVRanges
VCFEvaluateConstructor for class. Calls constructor for class. Using...
VCFQAParamUser Constructor for class. Call limits are set as default...
VCFQAParam-classDeclare class VCFQAParam which will store thresholds to apply...
VCFQAReport-classDeclare class VCFQAReport which will evaluate a VCF stored as...
genotypeeval documentation built on May 2, 2018, 4:06 a.m.