config_df               Default parameters of config.
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
getSNVRate              SNV percentage
getSkewness             Get absolute value of skewness
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
rmCNVinVCF              Remove CNV regions within VCF files given cnv
                        file
rmChangePoint           Remove CNV regions within VCF files by
                        changepoint method
sssc                    Same Species Sample Contamination
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.
