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Hey Michael,
One mode that might be useful is to change the stacking mode to Paired End. If there is a tandem duplication, you may see it in the boundaries where paired-end reads that span it don't find the standard distribution for distance between the paired end reads or if there is an inversion you don't see one of a forward and reverse strand being paired.
Click the little gear icon in the GB Pile-up plot and switch Stack mode to Paired End.
I hope that helps! Happy hunting! Gabe
