Re: [Samtools-help] Error rate by cycle

[Petr D. <pd...@sa...>]

Hi Peter,

sorry for the delay in replying, bamcheck has been now added to
samtools' git repository.

Best,
Petr


On Mon, 2012-03-19 at 20:59 +0000, White, Peter wrote:
> Thanks Petr - it would definitely be useful for my group. The plot you
> sent is exactly what I was trying to create, with the added bonus of
> breaking it down into base qualities.
> 
> Cheers,
> 
> Peter
> 
> -----Original Message-----
> From: Petr Danecek [mailto:pd...@sa...] 
> Sent: Thursday, March 15, 2012 4:44 AM
> To: Tim Fennell
> Cc: White, Peter; sam...@li...
> Subject: Re: [Samtools-help] Error rate by cycle
> 
> Hi Peter,
> 
> in our QC we routinely use 'bamcheck' to extract various stats from BAMs and to plot graphs, one of them being the number of mismatches by read cycle (attached). If people would find it useful, we can make it available or maybe add it to the samtools/misc..?
> 
> Best,
> Petr
> 
> 
> On Mon, 2012-03-12 at 09:18 -0400, Tim Fennell wrote:
> > Hi Peter,
> > 
> > We don't release that externally because it is a tool for detecting specific control sequences that we use at Broad.  For general evaluation we tend to plot quality score by cycle after base quality score recalibration as a way to visualize error rate by cycle, using the publicly available tool.
> > 
> > -t
> > 
> > On Mar 7, 2012, at 4:24 AM, White, Peter wrote:
> > 
> > > I would like to plot error rate by cycle using a bam file as input. Does Picard or SAM tools have this functionality?  In slide 8 of the Picard presentation I found there is an example using "CollectInternalControlMetrics.jar" but  this appears to not be part of the current software:
> > > 
> > > http://www.broadinstitute.org/files/shared/mpg/nextgen2010/nextgen_f
> > > ennell.pdf
> > > 
> > > Thanks
> > > 
> > > Peter
> 
> 
> 
> 
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-- 
 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.