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Naive question. I do not quite understand in what situations the postprocessing option -g would be useful (use gapped alignments when attempting to rescue pairs). Thoughts?
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If you are trying to rescue the other read considering the to-be-rescued end with indels the gapped method is useful. I find that it overfits by calling falsely indels in many cases. Remember, the rescue relies solely on its pair/mate.Originally posted by Protaeus View Post
I would test both out and see which you are most happy with. Always good to have options (literally).
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