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GATK 4 spark tools vs non-spark tools
I just started experimenting with GATK 4. In particular running through the spark tools (LOCAL). Am I missing something or is it not possible to go from spark tools for pre-processing (BwaAndMarkDuplicatesPipelineSpark + BQSRPipelineSpark) to the non-spark haplotype caller without sorting the bam file out of band b/c spark tools don't create a sorted bam file?