genotypeeval: QA/QC of a gVCF or VCF file

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Takes in a gVCF or VCF and reports metrics to assess quality of calls.

Author
Jennifer Tom [aut, cre]
Date of publication
None
Maintainer
Jennifer Tom <tom.jennifer@gene.com>
License
file LICENSE
Version
1.4.0

View on Bioconductor

Man pages

admixture
admixture - estimate admixture components using supervised...
callbyChrPlot
Dot plot of variant call counts (hom alt and het) by...
calltypePlot
Bar plot of variants (counts)
chunkData
chunkData is a private function to read in a chunk and...
computeTiTv
Private function to calc transition tranversion (titv) ratio
didSamplePass
Getter for VCFEvaluate class to check if Sample Passed....
didSamplePassOverall
Getter for VCFEvaluate class to check if Sample Passed....
genotypeQualityPlot
Histogram of genotype qualities
getCoefs
Private function to calc coefficients for admixture
getName
Getter for VCFQAReport class to return filename slot
getPlots
Getter for VCFQAReport class to return plots slot.
getResults
Getter for VCFQAReport class to return results. Return a...
getVR
getVr is a Getter. Returns vr slot.
goldCompare
Comparator to gold standard
GoldData-class
Declare class Gold to store information from Gold" (1000...
GoldDataFromGRanges
User Constructor for class. Used to associate the gold...
GoldDataParam
User Constructor for class
GoldDataParam-class
Declare class GoldDataParam which will store thresholds to...
hetGap
Gap between HETs by Chromosome
hetsMasked
Number hets in masked GRanges
homrefPlot
Dot plot of variant call counts (hom ref) by chromosome
meanGQ
Mean Genotype Quality (GQ)
myf
Private function to calc likelihood for admixture
numberCalls
Total Calls. This is the total number of calls in the file...
numberOfHets
Count Number of Hets
numberOfHomRefs
Count Number of Hom Ref
numberOfHomVars
Count Number of Hom Vars
percentHets
Percent of Hets as Total number of variants
percentInTarget
percent in target range read depth For 15 to 60 for 30x (50...
rareCompare
Comparator to rare variants. Rare is defined as 0.01 percent...
readDepth
Median read depth
readdepthPlot
Histogram of read depth by GT
ReadGoldData
User Constructor for class
ReadVCFData
User Constructor for class. Calls VCFData constructor:...
ReadVCFDataChunk
User Constructor for class. Calls VCFData constructor:...
readVcfGold
Private method for class. Read in Gold file - will read in...
reformatData
Take in the results from the population data and re-format it
titv
Transition transversion ratio in coding and non-coding
VCFData-class
Declare class Reads in VCF using readVCFAsVRanges
VCFEvaluate
Constructor for class. Calls constructor for class. Using...
VCFQAParam
User Constructor for class. Call limits are set as default...
VCFQAParam-class
Declare class VCFQAParam which will store thresholds to apply...
VCFQAReport-class
Declare class VCFQAReport which will evaluate a VCF stored as...

Files in this package

genotypeeval/DESCRIPTION
genotypeeval/LICENSE
genotypeeval/NAMESPACE
genotypeeval/R
genotypeeval/R/GoldData.R
genotypeeval/R/GoldDataParam.R
genotypeeval/R/PopulationSummary.R
genotypeeval/R/VCFData.R
genotypeeval/R/VCFQAParam.R
genotypeeval/R/VCFQAReport.R
genotypeeval/build
genotypeeval/build/vignette.rds
genotypeeval/inst
genotypeeval/inst/NEWS.Rd
genotypeeval/inst/doc
genotypeeval/inst/doc/genotypeeval_vignette.R
genotypeeval/inst/doc/genotypeeval_vignette.Rmd
genotypeeval/inst/doc/genotypeeval_vignette.html
genotypeeval/inst/ext-data
genotypeeval/inst/ext-data/chr22.GRCh38.vcf.gz
genotypeeval/inst/ext-data/chr22.GRCh38.vcf.gz.tbi
genotypeeval/inst/ext-data/example_gold_file.vcf
genotypeeval/man
genotypeeval/man/GoldData-class.Rd
genotypeeval/man/GoldDataFromGRanges.Rd
genotypeeval/man/GoldDataParam-class.Rd
genotypeeval/man/GoldDataParam.Rd
genotypeeval/man/ReadGoldData.Rd
genotypeeval/man/ReadVCFData.Rd
genotypeeval/man/ReadVCFDataChunk.Rd
genotypeeval/man/VCFData-class.Rd
genotypeeval/man/VCFEvaluate.Rd
genotypeeval/man/VCFQAParam-class.Rd
genotypeeval/man/VCFQAParam.Rd
genotypeeval/man/VCFQAReport-class.Rd
genotypeeval/man/admixture.Rd
genotypeeval/man/callbyChrPlot.Rd
genotypeeval/man/calltypePlot.Rd
genotypeeval/man/chunkData.Rd
genotypeeval/man/computeTiTv.Rd
genotypeeval/man/didSamplePass.Rd
genotypeeval/man/didSamplePassOverall.Rd
genotypeeval/man/genotypeQualityPlot.Rd
genotypeeval/man/getCoefs.Rd
genotypeeval/man/getName.Rd
genotypeeval/man/getPlots.Rd
genotypeeval/man/getResults.Rd
genotypeeval/man/getVR.Rd
genotypeeval/man/goldCompare.Rd
genotypeeval/man/hetGap.Rd
genotypeeval/man/hetsMasked.Rd
genotypeeval/man/homrefPlot.Rd
genotypeeval/man/meanGQ.Rd
genotypeeval/man/myf.Rd
genotypeeval/man/numberCalls.Rd
genotypeeval/man/numberOfHets.Rd
genotypeeval/man/numberOfHomRefs.Rd
genotypeeval/man/numberOfHomVars.Rd
genotypeeval/man/percentHets.Rd
genotypeeval/man/percentInTarget.Rd
genotypeeval/man/rareCompare.Rd
genotypeeval/man/readDepth.Rd
genotypeeval/man/readVcfGold.Rd
genotypeeval/man/readdepthPlot.Rd
genotypeeval/man/reformatData.Rd
genotypeeval/man/titv.Rd
genotypeeval/tests
genotypeeval/tests/testthat
genotypeeval/tests/testthat.R
genotypeeval/tests/testthat/testQA.R
genotypeeval/vignettes
genotypeeval/vignettes/genotypeeval_vignette.Rmd
genotypeeval/vignettes/my.bib