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best order of mark duplicates, local realignment and recalibration
I am wondering what is the best order of dedup, local realn, and recal what factors to consider when coming up with the order. The GATK best practices recommend different orders when dealing with per lane or per sample processing. I would natively think that realignment should proceed dedup because it may change the alignment coordinates. And recalibration should come last because some of the model fitting may assume independence? Does the order really matter any way?