Question: Why does samtools calmd change the NM tag when generating the MD tag?
gravatar for francois
27 days ago by
francois10 wrote:

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 (, I don't understand the logic behind it.

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

sequencing • 86 views
ADD COMMENTlink written 27 days ago by francois10

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

ADD REPLYlink written 27 days ago by Pierre Lindenbaum129k

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
ADD REPLYlink modified 27 days ago • written 27 days ago by francois10
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