Variant Quality Investigation Helper

Documentation for package ‘vanquish’ version 1.0.0

config_df	Default parameters of config.
defcon	DEtection of Frequency CONtamination
generate_feature	Feature Generation for Contamination Detection Model
getAlt2	Second alternative allele percentage
getAnnoRate	Annotation rate
getAvgLL	Calculate average log-likelihood
getLowDepth	Low depth percentage
getRatio	Get the ratio of allele frequencies with a region
getSkewness	Get absolute value of skewness
getSNVRate	SNV percentage
getVar	Calculate zygosity variable
locateFile	Check input filename
negll	Negative Log Likelihood
readGATK	Read in input vcf data in GATK format for Contamination detection
readStrelka	Read in input vcf data in strelka2 format for Contamination detection
readVarDict	Read in input vcf data in VarDict format for Contamination detection
readVarPROWL	Read in input vcf data in VarPROWL format
read_vcf	VCF Data Input
rho_est	Estimate Rho for Alternative Allele Frequency
rmChangePoint	Remove CNV regions within VCF files by change point method
rmCNVinVCF	Remove CNV regions within VCF files given cnv file
summary_vcf	VCF Data Summary
svm_class_model	Default svm classification model.
svm_regression_model	Default svm regression model.
train_ct	Train Contamination Detection Model
update_vcf	Remove CNV regions within VCF files
vcf_example	VCF example file.