Re: [Samtools-help] problem with samtools mpileup

[Federico Abascal]

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  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. 
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research 
> Limited, a charity registered in England with number 1021457 and a 
> company registered in England with number 2742969, whose registered 
> office is 215 Euston Road, London, NW1 2BE. 
> 
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Re: [Samtools-help] problem with samtools mpileup

[James Bonfield]

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. 


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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