Hi there,
following this suggestion I’ve converted the results of a number of analyses into VCF files.
I believe however I never exploited the full potential of the VCF object and I’m not sure which would be the most efficient way for a targeted query, i.e. check if a variant from a VCF object is present in any of the others, like I would to with an SQL database.

Ideally, I’d like to add a metadata field to one of my objects, that could be reported in the INFO field like any other annotation when I then write the VCF on a file.
To do this I’d have to add the field both in the info(header(vcf)) and in the info(vcf), with/after the result of my query.

Two questions therefore:
1) how do you add an INFO field in a way that doesn’t generate error from within R

2) what’s the most computationally efficient way to query for presence/absence of a variant (I thought about a match on the names, a countOverlaps on the GRanges etc, but that doesn’t exploit the tabix index, and still seems to me a bit clumsy).

thanks for any advice on how to best use this class,
best
Francesco



On 3 Oct 2013, at 15:53, Vincent Carey <stvjc@channing.harvard.edu<mailto:stvjc@channing.harvard.edu>> wrote:




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