# SomaticCallers


Recipe source code: https://github.com/rworkflow/RcwlRecipes/blob/master/Rcwl/pl_SomaticCallers.R (opens new window)

# plot

## SomaticCallers

# Inputs

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