[Bioc-sig-seq] R453Plus1Toolbox

Hans-Ulrich Klein h.klein at uni-muenster.de
Wed Feb 16 18:02:18 CET 2011

Hi Dave,

that is right. The manual of Roche's AVA software says: "The automatic 
Variant detection does not currently report insertions or monomer 
deletions shorter than 3 bases." At this time, the R453Plus1Toolbox does 
not implement an indel calling algorithm but relies on the results 
reported by the AVA software.
Since it seems that Roche is not going to solve this issue, we have this 
topic on our to-do list for our package.


On 16/02/11 13:43, David A. wrote:
> Hi, I have found a package called R453Plus1Toolbox for analysis of Roche's sequencing data. As far as I know, using AVA, 1bp indels are filtered off fro mthe results to avoid false positives. They can be seen by going to the flowgrams of the region, but they are not part of the output table. Does anyone know if R453Plus1Toolbox can detect them?
> Thanks,
> Dave
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Hans-Ulrich Klein
Institute of Medical Informatics
University of Münster
Domagkstraße 9
48149 Münster, Germany
Tel.: +49 (0)251 83-58405

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