Man pages for sssc
Same Species Sample Contamination Detection
| 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... |
| readStrelka | Read in input vcf data in strelka2 format for Contamination... |
| readVarDict | Read in input vcf data in VarDict format for Contamination... |
| 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. |
