On Thu, Oct 3, 2013 at 7:18 AM, Francesco Lescai <
francesco.lescai@hum-gen.au.dk> wrote:

> Hi guys,
> I would like to store lists of variants (SNPs and INDELs) in a convenient
> format to be used frequently with other bioconductor packages, and I was
> thinking to store them as Annotation databases.
> In this way I could store and query my own list of variants with
> annotations coming from my work and/or previous experiments.



>
>
Most of the examples/vignettes I could find like SQLForge are however
> gene-centric.
> Can I create a custom one, maybe using SNPlocs as template?
>
>
Have you considered tabix-indexed VCF?  This can be stored in a package and
Rsamtools/VariantAnnotation facilities can be used for targeted querying.
 The SNPlocs containers are likely to be redesigned in the near future.


> thanks for any suggestions,
> Francesco
>
>
>
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