# BaseRecal
Recipe source code: https://github.com/rworkflow/RcwlRecipes/blob/master/Rcwl/pl_BaseRecal.R (opens new window)
# plot
# Inputs
| label | type | description | |
|---|---|---|---|
| bam | File | ||
| ref | File | ||
| knowSites | array | ||
| oBam | string |
# Outputs
| label | type | description | |
|---|---|---|---|
| rcBam | File | ||
| flagstat | File | ||
| stats | File |
# steps
| label | doc | |
|---|---|---|
| BaseRecalibrator | ||
| ApplyBQSR | ||
| samtools_index | ||
| samtools_flagstat | ||
| samtools_stats |