Question on bwa options about sniffles HOT 5 CLOSED

Hi
thanks for reaching out and trying Sniffles.
I am using the best and second best alignment score fields to get a better estimate about the reliability of the read. (AS, XS) Furthermore I am using the tag which reports the secondary alignments (SA).

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Those seem to be present by default in the current bwa-mem (bwa 0.7.13). Should we be running it any special way? Like, with any of these:

-a output all alignments for SE or unpaired PE
-Y use soft clipping for supplementary alignments
-M mark shorter split hits as secondary

... ?

from sniffles.

Yes the best thing is to run -M and -x with pacbio or ont2d.
You can also try our own mapper NGM-LR ;)

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Thanks Fritz!
I actually did switch to NGM-LR, since Sniffles wasn't able to open my BAM files produced by bwa-mem ... maybe because of lack of the -M option.
With NGM-LR, I ran pretty much default (-t 10 -x pacbio -i 0.75 ... nothing that should affect SAM line content) and Sniffles ran fine.

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Mhm strange. Was it sorted? Do you have the cmd output from Sniffles using bwa-mem?

The -M option just gives me the information which aligned segment is the primary and thus avoids that I process one read more then one time.
Thanks for trying NGM-LR. Let me know If you have a hint on what when wrong with the bwa-mem results. I am testing Sniffles usually on both.
Thanks

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