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 |
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 changepoint method |
rmCNVinVCF |
Remove CNV regions within VCF files given cnv file |
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. |