Question: custom variant AnnotationDbi?
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gravatar for Lescai, Francesco
6.2 years ago by
Denmark
Lescai, Francesco380 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? thanks for any suggestions, Francesco [[alternative HTML version deleted]]
annotation snplocs • 466 views
ADD COMMENTlink modified 6.2 years ago by Vincent J. Carey, Jr.6.3k • written 6.2 years ago by Lescai, Francesco380
Answer: custom variant AnnotationDbi?
0
gravatar for Vincent J. Carey, Jr.
6.2 years ago by
United States
Vincent J. Carey, Jr.6.3k wrote:
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 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.2 years ago by Vincent J. Carey, Jr.6.3k
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