# bwaMRecal


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

# plot

## bwaMRecal

# Inputs

label type description
outBam string
RG string
threads int
Ref File
FQ1s File
FQ2s File?
knowSites array

# Outputs

label type description
BAM File
matrix File
flagstat File
stats File

# steps

label doc
bwaAlign
markdup
BaseRecal