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changing MAPQs in aligned bam files
I use a pipeline of Picard's MarkDuplicates, RealignTargetCreator, IndelRealigner, BaseRecalibrator, PrintReads. I noticed a small but consistent increase in reads with MAPQ >= 20 from the initial bam file to the final bam file. Any idea where this could be happening? I didn't think any of those tools changed MAPQ, but I'm assuming I'm wrong.