This workflow preprocesses short read flowcell data in preparation for variant calling. This workflow contains the following steps: 1) Sam → Fastq (if necessary), 2) Alignment to reference with bwa-mem2 (GitHub - bwa-mem2/bwa-mem2: The next version of bwa-mem), 3) Mark Duplicate reads, 4) Recalibrate base quality scores.
This is a companion discussion topic for the original entry at github.com/broadinstitute/PTA_Analysis/01_PTAAlignmentWorkflow_decontamination