Why does samtools calmd change the NM tag when generating the MD tag?

Question

[francois]

I used samtools calmd to generate MD tags.

While it was running, I noticed it started changing NM tags in my bam file. For example:

[bam_fillmd1] different NM for read '783b5c4e-8ef2-469f-b278-ead281a35278': 72 -> 1074

While this behaviour seems normal (http://www.htslib.org/doc/samtools-calmd.htm), I don't understand the logic behind it.

Why does samtools calmd changes NM tags while generating MD tags?

[Pierre Lindenbaum]

are you sure about the reference sequence ? is it the very same that the one used to map the reads ?

[francois]

Yes. Just as a sanity check:

Alignment command was

minimap2 -ax map-ont hg38.fa \
      110618_pool.fastq.gz > 110618.sam

Then samtools view / sort / index

And now:

samtools calmd 110618s.bam hg38.fa -b > 110618smd.bam