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Class Summary |
| CallMpileup |
A class for calling variants or consensus bases from a pileup file |
| CallPileup |
A class for calling variants or consensus bases from a pileup file |
| Comparison |
A class for comparing positions (variants) between two files |
| CopyCaller |
A DEPRECATED class for calling copy number variants from somatic copynumber output |
| Copynumber |
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| Coverage |
A class for assessing coverage of target regions (experimental) |
| FilterSomatic |
A class for filtering VarScan variant predictions |
| FilterVariants |
A class for filtering VarScan variant predictions |
| FishersExact |
A statistical class for performing Fisher's exact test. |
| LimitVariants |
A class for restricting a list of variants to a given set of positions or regions |
| ProcessSomatic |
A class for processing VarScan output by somatic status and confidence |
| ReadCounts |
A class for obtaining read counts for a list of variants |
| Somatic |
A class for determining somatic status of variants from Normal/Tumor pileup files |
| VarScan |
A set of tools for variant detection in next-generation sequence data. |