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So looking back at a previous analysis, I noticed that BaseRecalibrator took about 16 hours, but then PrintReads took another 48, which seems egregious.
My plan is to run PrintReads separately on different loci, each using the "merged" table from BaseRecalibrator, and then merge the resulting BAM files.
I'd be surprised if this isn't equivalent to running PrintReads on the whole genome at once, but I just wanted to check with the experts here.