Bwa-mem uses global alignment in aligned regions to reconstruct CIGAR at the end. It doesn't support glocal alignment.

Minimap2 implements a similar but not identical algorithm, but this difference might emulate glocal alignment to some extent. To try that, you may use a large "--end-bonus" like

minimap2 -axsr --end-bonus=100

It worked on a toy example I tried. Please beware that you often need to filter out poor glocal alignments as they may be not real.

Thanks @lh3 I'll see how it goes.

Dear @tseemann, how did it go?

@sdwfrost i never really got back to it. in fact i completely lost track of this. thanks for the reminder!
Another lesson in map minimap2 having more info than minimap2 --help