I have genotyping data coming from GenomeStudio (Illumina) software from a SNP-chip, and I would like to convert this data to VCF. Does anyone know of a tool to do this? or should I write my own script to do this?

Here is how the GenomeStudio output file is formatted:

    Index    Name           Address      Chr    Position     GenTrain Score   Sample1 Sample2
    1        cnvi0000001    124680304    5      164388439    0                AA      AB
    ...


Genomestudio has a [PLINK export plugin][1], and you can use [PLINK/SEQ][2] to convert that format to a VCF.

 [1]: http://support.illumina.com/downloads/plink_input_report_plug-in_v213.ilmn
 [2]: https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fatgu.mgh.harvard.edu%2Fplinkseq%2F