Based on https://github.com/tjiangHIT/cuteSV/issues/4#issue-647402670, it would be convenient to add the --MD tag to the minimap2-based alignments generated by VISOR LASeR, as this is required by some SV callers. I'll also add the --cs tag to the default alignment. Not sure that using soft clipping for supplementary alignments (-Y) is what most people expect as the default behaviour.
Based on https://github.com/tjiangHIT/cuteSV/issues/4#issue-647402670, it would be convenient to add the --MD tag to the minimap2-based alignments generated by VISOR LASeR, as this is required by some SV callers. I'll also add the --cs tag to the default alignment. Not sure that using soft clipping for supplementary alignments (-Y) is what most people expect as the default behaviour.