Samtools - Calmd Errors - Different Nm For Read

Question

[Applet]

I'm trying to put MD tags into my BAM file by calling samtools calmd like so:

samtools calmd -u update_reads-aligned-parent2.sorted.bam parent2.fa > update_reads-aligned-parent2.sorted.calmd.bam

It is generating a file that seems acceptable but I'm getting output like this in stderr:

[bam_fillmd1] different NM for read 'SRR074288.8752612': 0 -> 22
[bam_fillmd1] different NM for read 'SRR074288.12122138': 0 -> 5
[bam_fillmd1] different NM for read 'SRR074288.11769308': 1 -> 11
[bam_fillmd1] different NM for read 'SRR074288.574781': 24 -> 65
[bam_fillmd1] different NM for read 'SRR074288.1022883': 0 -> 54
[bam_fillmd1] different NM for read 'SRR074288.18304607': 5 -> 53

(I'm on Version: 0.1.7 (r510) of Samtools.)

Does anyone know what could be going on?

Answer 1

[brentp]

That's just telling you the adjustments it made, those are not errors.

BTW, I think by now it's recommended to use -E for higher sensitivity, the default err's on the side of specificity.

EDIT: More explanation from lh3: http://sourceforge.net/mailarchive/message.php?msg_id=28933512

And re calmd, the docs even say it edits the NM tag: http://samtools.sourceforge.net/samtools.shtml

I assume this is because it changes things around indels, but I did not read the code.

[Applet]

Thanks. But there are millions of these "errors/messages". On most of my runs I haven't seen any. (The difference in this case is Stampy generated the SAM files instead of BWA.) Also what is making the adjustments? Shouldn't the calmd command simply add in MD tags? Why does it need to adjust anything.

[Applet]

Also what do you mean by specificity vs sensitivity?

[Applet]

@brentp, bump .. I'm stuck