Re: [Samtools-help] Error rate by cycle

[Tim F. <tfe...@br...>]

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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