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.
samtools calmd changes NM tags while generating MD tags?