Suppose we have a 30bp-50bp deletion, and read length is 100bp. If the read happens to cover the deletion, I'm just wondering, will BWA align the read with soft-clipped sequences, or allow this 30bp-50bp gap?

I'm pretty much sure for deletion like 10bp or even up to 20bp, BWA can do the gapped alignment; and for deletions, say 70, 80bp, BWA will produce split reads. But I'm just confused about this middle state.

Thanks a lot!

thanks. But can you explain "fraction of gap opens" and "gap extensions" more?