# targetVarCall
Recipe source code: https://github.com/rworkflow/RcwlRecipes/blob/master/Rcwl/pl_targetVarCall.R (opens new window)
# plot
# Inputs
| label | type | description | |
|---|---|---|---|
| Sample | string | ||
| RG | string | ||
| threads | int | ||
| Ref | File | ||
| FQ1 | File | ||
| FQ2 | File | ||
| knowSites | array | ||
| bed | File | ||
| downsampling | int |
# Outputs
| label | type | description | |
|---|---|---|---|
| BAM | File | ||
| flagstat | File | ||
| stats | File | ||
| gVCF | File | ||
| VCF | File |
# steps
| label | doc | |
|---|---|---|
| bwaAlign | ||
| BaseRecal | ||
| bedtolist | ||
| HaplotypeCaller | ||
| GenotypeGVCFs |