making clips more favourable than matching (and reducing secondary mappings)

[kcajj]

Hello, I have a very specific proble regarding the mapping of some special ONT reads. These reads are sometimes made of a part with an high mutation density and another part with low mutation density.

right now minimap2 with default options for ONT is mapping these reads for their whole length.

What I would like to achieve is that the reads mentioned above map only in the part with low mutation density and the other part is softclipped. at the same time, I would like to have secondary mappings only if the mutation density is very low.

I tried to play a bit around with the score function of minimap (i tried to use the score settings of asm5: -A 1 -B 19 -O 39,81 -E 3,1) but either i get some errors or the output doesn't change as much as i would like.

Maybe someone knows enough about minimap2 parameters to help me.

Thank you.