This Biowdl workflow will preprocess a BAM file, preparing it for variantcalling based on the GATK Best Practises.
You can find the documentation here.
This workflow is part of Biowdl, developed by the SASC team at Leiden University Medical Center.
For any question related to this workflow, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.