Re: [SO-devel] new array platform for ##technology-platform-name - how to cenvert from beadarray data to gvf?

[Barry M. <bar...@ge...>]

Hi Lauro,

We've developed a perl library as part of the SO project, that among other things has a lot of parsers that convert various types of data files into GFF3 and GVF.  I don't have a download link up for it on the SO website quite yet because I need to add a bit more functionality and update the docs a bit, but if you're familiar with perl and don't mind working with prerelease code I'd be happy to set you up for a download.  The parsers are all small subclasses that override a couple of methods in which you describe the structure of the document format that you want to convert, so it's pretty easy to add a new parser.  If you send a hundred lines or so of your Infinium output I'd be happy to look it over and either write the subclass for you or at least provide help if I'm not able to get to writing it myself soon enough to fit your schedule.


I've added your new Exome bead chip to the GVF spec.  It's currently in the provisional 1.07 version of the spec (http://www.sequenceontology.org/resources/gvf_1.07.html), but feel free to start using the name you suggested right away as I don't see any reason why it won't be included in the next spec release.

Thanks for the feedback

Barry

On Feb 19, 2013, at 3:13 AM, Lauro Sumoy wrote:

> Hello,
>  
> I am trying to figure out how to convert Illumina infinum genotyping data into gvf (or vcf). Is there any script or tool that does conversion from finalreprort format into gvf or vcf?
>  
> We are using HumanExome v1.0 beadchips. Can you please add this to the possible supported values for array platforms listed in http://www.sequenceontology.org/resources/gvf.html?
>  
> HumanExome_1.0: Illumina BeadChip HumanExome 1.0
>  
> Thank you,
>  
> Lauro
>  
> Lauro Sumoy
> Institute of Predictive and Personalized Medicine of Cancer
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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
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