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Why do BAM files have to be correctly formatted before Picard RevertSam?
After completing tutorial #6483 on mapping and cleaning up short read data efficiently, I tried this with our lab's own BAM files. However, when completing the first step (generate a uBAM from an aligned BAM), I found that I had to use Picard CleanSam and AddOrReplaceReadGroups in order for RevertSam to properly work. I was under the impression that the workflow in the tutorial would be used, at least partially, for BAM files that are not properly formatted for GATK analysis. Is there an intuition as to why I had to format the original BAM file before beginning this process? It seems like those steps could be done after realigning with bwa mem.