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

[Dan B. <dbo...@gm...>]

Sounds useful! (CC'ing the VCF list).

Cheers,
Dan.
On Feb 19, 2013 9:14 PM, "Barry Moore" <bar...@ge...>
wrote:

> 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****
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> Barry Moore
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