On Thu, Apr 20, 2017 at 03:52:11PM +0900, kenichi chiba wrote:
> I would like to ask for help about samtools mpileup. The output of 
> samtools mpileup may differ depending on the presence or absence of the 
> -f option. If there are probably about 20 bp deletions, some deletions 
> are missing from the output.

I shudder any time I see questions about mpileup as it's such a
complex thing to describe with many many options!

However first of all I would suggest trying samtools 1.4.  1.2 is
pretty old now.  Not that I expect mpileup has changed a great deal,
but it's an obvious first check to do.

The other things to try would be turning on and off the various
mpileup options (-B in particular, but maybe others) to see what
impact they have.  If you can spot one specific option which is the
cause of the difference between with-ref and without-ref then you're
closer to understanding why.  My gut instinct is it will be the BAQ


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