Restrictive alignment with minimap2

Question

[njornet]

I need to align nanopore reads from human to a custom reference genome and I want to align only the reads that have a very high identity. I tried changing the missmatch penalty but if I increase it too much minimap raises a Segmentation fault error. Should I change something else in the configuration of minimap2 or should I filter the aligned reads by score or something and how would I do that?

Thank you!

[GenoMax]

I want to align only the reads that have a very high identity

Filtering after the fact based on MAPQ or CIGAR's an option?

[njornet]

If I have the resulting SAM it is right?