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--dontUseSoftClippedBases option seems to involve non-softclipped bases


I am checking the differences between the calls with/without using soft clipped bases.
Some of the missed calls when '--dontUseSoftClippedBases=true' (compared with the calls when 'false') harbored in the middle of the reads, not in the soft-clipped bases.
Why the calls were missed?
Many thanks!!


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