Man pages for sssc
Same Species Sample Contamination Detection

config_dfDefault parameters of config.
generate_featureFeature Generation for Contamination Detection Model
getAlt2Second alternative allele percentage
getAnnoRateAnnotation rate
getAvgLLCalculate average log-likelihood
getLowDepthLow depth percentage
getRatioGet the ratio of allele frequencies with a region
getSkewnessGet absolute value of skewness
getSNVRateSNV percentage
getVarCalculate zygosity variable
locateFileCheck input filename
negllNegative Log Likelihood
readGATKRead in input vcf data in GATK format for Contamination...
readStrelkaRead in input vcf data in strelka2 format for Contamination...
readVarDictRead in input vcf data in VarDict format for Contamination...
readVarPROWLRead in input vcf data in VarPROWL format
read_vcfVCF Data Input
rho_estEstimate Rho for Alternative Allele Frequency
rmChangePointRemove CNV regions within VCF files by changepoint method
rmCNVinVCFRemove CNV regions within VCF files given cnv file
ssscSame Species Sample Contamination
summary_vcfVCF Data Summary
svm_class_modelDefault svm classification model.
svm_regression_modelDefault svm regression model.
train_ctTrain Contamination Detection Model
update_vcfRemove CNV regions within VCF files
vcf_exampleVCF example file.
sssc documentation built on May 2, 2019, 4:03 p.m.