Question

Plugins in ensemblVEP

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Hi Valerie, is there a way to specify the "--plugin" argument for varianteffectpredictor.pl via the VEPParam function ? If not, would it be possible to add it ? I am referring to plugins as described here: http://uswest.ensembl.org/info/docs/variation/vep/vep_script.html#plug ins Thanks a lot ! Thomas -- output of sessionInfo(): NA -- Sent via the guest posting facility at bioconductor.org.

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ADD COMMENT • link updated 11.8 years ago by Valerie Obenchain ★ 6.8k • written 11.9 years ago by Guest User ★ 13k

score 0 · Answer 1 · 2013-05-07

Hi Thomas, No, the plugins aren't currently implemented ... neither are the database/cache options. They are on the TODO and I'll try to get them next week. Valerie On 05/07/13 11:31, Thomas Sandmann [guest] wrote: > Hi Valerie, > > is there a way to specify the "--plugin" argument for varianteffectpredictor.pl via the VEPParam function ? If not, would it be possible to add it ? > > I am referring to plugins as described here: > http://uswest.ensembl.org/info/docs/variation/vep/vep_script.html#pl ugins > > Thanks a lot ! > Thomas > > -- output of sessionInfo(): > > NA > > -- > Sent via the guest posting facility at bioconductor.org. >

score 0 · Answer 2 · 2013-05-29

The --plugin argument is implemented in ensemblVEP 1.1.3. I've also added support for the caching options. How are the new rownames from readVcf() working out? Any further problems with the VCFRowID? Valerie On 05/07/2013 11:31 AM, Thomas Sandmann [guest] wrote: > Hi Valerie, > > is there a way to specify the "--plugin" argument for varianteffectpredictor.pl via the VEPParam function ? If not, would it be possible to add it ? > > I am referring to plugins as described here: > http://uswest.ensembl.org/info/docs/variation/vep/vep_script.html#pl ugins > > Thanks a lot ! > Thomas > > -- output of sessionInfo(): > > NA > > -- > Sent via the guest posting facility at bioconductor.org. >