Looks like no one has actually read the question correctly. PAF is missing lots of information compared to SAM, because it is a summary of alignment, but it also has easy access to the alignment start and stop coordinates, sequences lengths, etc. Since PAF is less information-dense you cannot convert in both directions, but there's no reason why you can't convert from SAM to PAF.

There are several options:

1. Use Heng Li's experimental toolkit, htsbox samview -p in.bam: https://github.com/lh3/htsbox
2. Use paftools sam2paf: https://github.com/lh3/minimap2/blob/master/misc/README.md#introduction
3. Use this python library: https://bioconvert.readthedocs.io/en/master/_modules/bioconvert/sam2paf.html

I've been looking for the answer to this question, and I am planning on using #2.

I'm not sure how "Matches" are interpreted, but the existence of a sam2paf converter implies that it probably counts all M operations (match "=" or mismatch "X") regardless of the true identity of the reference vs read within the Match block.

Yeah 2 out 3 answers do not address the question!

Thanks @rlorigro for the lead.

Just to provide a (hopefully) straightforward answer, this seems to work well for me:

paftools.js sam2paf in.sam > out.paf

It comes with minimap2, I did not have to install anything on my system.

FYI, paftools.js sam2paf alone returns

Usage: paftools.js sam2paf [options] <in.sam>

Options:

-p convert primary or supplementary alignments only

-L output the cs tag in the long form

Good luck!

There is no direct way to do that. Realignment is necessary, see the developers (Ih3) answer here: https://github.com/lh3/minimap2/issues/493 (the first hit when searching for convert sam to paf by the way...).

Here is a section that explains how: https://github.com/lh3/miniasm#getting-started