Thank you very much. Now I understand well. If the -B option is
specified, the missing deletion will be output. When the -f option is
not specified, mpileup is handled as -B Disable BAQ calculation.
Best regards,
Ken
On 2017/04/20 17:15, Federico Abascal wrote:
I asked this sometime ago… The reason is because when you provide the fasta
reference file, then BAQ is enabled. BAQ does realignment and base quality
score recalibration and results in different mpileup outputs. In my experience
BAQ is very good at removing false positives, but when the coverage is not
large enough it results in lots of true variation also being removed.
Best,
Federico
On 20 Apr 2017, at 08:52, James Bonfield <j...@sanger.ac.uk> wrote:
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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Kenichi Chiba
Human Genome Center
Institute of Medical Science
University of Tokyo
E-Mail: kch...@hgc.jp
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