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Queue allows for "per-region" parallelism using scatter-gather. However, not all GATK tools support this (e.g. RealignerTargetCreator), and not all tools in a pipeline are GATK tools (e.g. BWA).
What I would like to do in the 1st phase of the best-practice pipeline is "per-sample" parallelism, that is, process each sample in parallel on a separate cluster node. Is there a recommended way to do this?