genotypeeval: QA/QC of a gVCF or VCF file

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("genotypeeval")
AuthorJennifer Tom [aut, cre]
Bioconductor views BatchEffect DataImport Genetics SNP Sequencing VariantAnnotation
Date of publicationNone
MaintainerJennifer Tom <tom.jennifer@gene.com>
Licensefile LICENSE
Version1.4.0

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...

Functions

admixture Man page
callbyChrPlot Man page
calltypePlot Man page
chunkData Man page
computeTiTv Man page
didSamplePass Man page
didSamplePassOverall Man page
genotypeQualityPlot Man page
getCoefs Man page
getName Man page
getPlots Man page
getResults Man page
getVR Man page
goldCompare Man page
GoldData-class Man page
GoldDataFromGRanges Man page
GoldDataParam Man page
GoldDataParam-class Man page
hetGap Man page
hetsMasked Man page
homrefPlot Man page
meanGQ Man page
myf Man page
numberCalls Man page
numberOfHets Man page
numberOfHomRefs Man page
numberOfHomVars Man page
percentHets Man page
percentInTarget Man page
rareCompare Man page
readDepth Man page
readdepthPlot Man page
ReadGoldData Man page
ReadVCFData Man page
ReadVCFDataChunk Man page
readVcfGold Man page
reformatData Man page
titv Man page
VCFData-class Man page
VCFEvaluate Man page
VCFQAParam Man page
VCFQAParam-class Man page
VCFQAReport-class Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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