# Mutect2PL
Recipe source code: https://github.com/rworkflow/RcwlRecipes/blob/master/Rcwl/pl_Mutect2PL.R (opens new window)
# plot
# Inputs
| label | type | description | |
|---|---|---|---|
| tbam | File | ||
| nbam | File | ||
| Ref | File | ||
| normal | string | ||
| tumor | string | ||
| gresource | File | ||
| pon | File | ||
| interval | File | ||
| comvcf | File | ||
| filter | string | ||
| threads | int? |
# Outputs
| label | type | description | |
|---|---|---|---|
| filterVCF | File | ||
| passVCF | File | ||
| conTable | File | ||
| segment | File |
# steps
| label | doc | |
|---|---|---|
| Mutect2 | ||
| GetPileupSummariesT | ||
| GetPileupSummariesN | ||
| CalculateContamination | ||
| LearnReadOrientationModel | ||
| FilterMutectCalls | ||
| bcfview |
← MuSE scatter RSeQC →