# bwaMRecal
Recipe source code: https://github.com/rworkflow/RcwlRecipes/blob/master/Rcwl/pl_bwaMRecal.R (opens new window)
# plot
# 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 |
← AnnPhaseVcf bwa align →