Question: Samtools - Calmd Errors - Different Nm For Read
2
gravatar for Applet
8.5 years ago by
Applet150
Applet150 wrote:

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?

bam samtools sam • 3.9k views
ADD COMMENTlink written 8.5 years ago by Applet150
2
gravatar for brentp
8.5 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

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.

ADD COMMENTlink modified 8.4 years ago • written 8.5 years ago by brentp23k

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.

ADD REPLYlink written 8.4 years ago by Applet150

Also what do you mean by specificity vs sensitivity?

ADD REPLYlink written 8.4 years ago by Applet150

@brentp, bump .. I'm stuck

ADD REPLYlink written 8.4 years ago by Applet150
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 774 users visited in the last hour