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
calculations.
James
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
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