Re: [Samtools-help] Error rate by cycle

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

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_fennell.pdf
> > 
> > Thanks
> > 
> > Peter




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