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is there more context to this question or a reason you think they are not included by default?
Just want to compare how many bases I lose from clipping with different parameters
Hard to see how it's possible since soft-clipped bases technically don't have an aligned position... Maybe it would make sense to just input alignments from your different parameter runs to get the side-by-side coverage, e.g.
and then you could do some custom summary if needed.
Ya, I just settled on doing 'endtoend' alignments instead of 'local' so the bases aren't clipped
don't you mean