de-novo variant calling at 0.5% on Nanopore data

I can clearly see that there are 2 different haplotypes in my amplicon Nanopore data, but all the tools I found to denoise Nanopore data use global alignments and are not sensitive enough.
How can I denoise this alignment but keep the SNP information? I tried everything I found on google.
I can not simply make a consensus, because a consensus between a gap and another nucleotide would be N, so I would loose information.

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Hi Adrian,

Welcome to the forums!

This is a neat question; why can't you do SNP calling from an MSA?

As you discovered, Nanopore is noisy enough that Illumina aligners may not work.

But minimap 2 works great and that MSA looks okay, so this should be possible.

How did you make that MSA? What other output formats does that tool support?

Thank you for your reply.
From what I understand minimap2 is a local alignment reference mapper, but I have a global alignment, de-novo.
One .fasta file contains QCed amplicon data from just one gene.

I've not worked with Nanopore data like this, so I'm not 100% sure...

Maybe convert the MSA to a sam/bam alignment file like this, then run a SNP caller on it? I'm not sure there's a great way to do this from within Qiime2 right now.