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BAM with soft-clipped primer sequences as an input for RevertSam (Tutorial #6483)
Could I use RevertSam on primer-clipped BAM and then MergeBamAlignment using the primer-clipped BAM and uBAM originated from it as input?
I'm analyzing paired-end TruSeq Custom Amplicon panel data, thus the workflow includes soft-clipping primer sequences with BamClipper. How do I implement the soft-clipping step into the data cleaning pipeline offered in the Tutorial #6483?