SomaticCallers
Recipe source code: https://github.com/rworkflow/RcwlRecipes/blob/master/Rcwl/pl_SomaticCallers.R (opens new window)
plot
| label | type | description |
|---|
| tbam | | File | |
| nbam | | File | |
| Ref | | File | |
| dbsnp | | File | |
| gresource | | File | |
| pon | | File | |
| interval | | File | |
| comvcf | | File | |
| filter | | string | |
| threads | | int | |
Outputs
| label | type | description |
|---|
| mutect2filterVCF | | File | |
| mutect2passVCF | | File | |
| mutect2conTable | | File | |
| mutect2segment | | File | |
| MuSEout | | File | |
| strelka2snv | | File | |
| strelka2indel | | File | |
| SomaticSniperout | | File | |
| VarDictout | | File | |
| VarScanSnp | | File | |
| VarScanIndel | | File | |
| VarScansVcf | | File | |
| mergeTSVout | | File | |
| WrapperSNV | | File | |
| WrapperINDEL | | File | |
| WrapperESNV | | File | |
| WrapperEINDEL | | File | |
| neusomaticVCF | | File | |
steps
| label | doc |
|---|
| Mutect2PL | | |
| MuSE | | |
| bgzip | | |
| tabixIndex | | |
| mantaStrelka | | |
| SomaticSniper | | |
| VarDict | | |
| VarScanPL | | |
| Wrapper | | |
| mergeTSV | | |
| neusomaticPL | | |