minimap2 hard clipping around large indels, parameter suggestions

I am mapping telomere containing reads in which the reference may have a large indel right at junction of telomere and non-telomere sequence and the reads are getting hard clipped but I want them to go across that indel into the telomere. I have tried asm10 and asm20, and then lowering gap penalty O7,11 which helps for some smaller indels but still not mapping the length of the read. Is there any suggestions on what parameters to get the length of the read to map with large indels into a repeat region for one part of the read?

version: 2.24-r1122

Sep 27 '22 09:09 rob234king

How long is the gap? Is it insertion or deletion?

Sep 28 '22 01:09 lh3

It can be either depending upon subtelomere but typically I see a deletion in relation to the reference. Largest is 2kbp but most are below 500bp.

Sep 28 '22 10:09 rob234king

I assume you are using long reads. HiFi or Nanopore? What is the read length? It would also be good to show me a couple of examples.

Sep 28 '22 14:09 lh3

Could you please share an email and I'll forward on some more detailed information with screenshots?

Sep 30 '22 14:09 rob234king