[ensembl-dev] VEP: Is it possible to add LRG annotations?

[Will McLaren]

Hi Andrew,

In fact this is already possible; just add the flag --lrg at runtime. Note
however that using LRGs depends on connecting to our database, so this will
not work using --offline and will connect to ensembldb.ensembl.org when
using --cache. Because of this database connection you may find that the
script runs more slowly as it attempts to remap your input variants to LRG
coordinates.

I'm afraid this is missing from the documentation currently, I will get
that updated.

Regards

Will McLaren
Ensembl Variation


On 31 March 2014 22:24, Andrew Carson <acarson at invivoscribe.com> wrote:

> Hi ensembl-dev team,
>
> I was just wondering if there are plans to incorporate the LRG (locus
> reference genomic) records into the VEP annotation pipeline (from here:
> http://www.lrg-sequence.org/home). I only ask because in the HGVS new
> clinical reporting guidelines they recommend using the LRG sequence (if one
> is present) to standardize variant reporting.
>
>
>
> It would also be very useful to have an option where, if a variant
> overlaps an LRG, you can choose to "pick" that consequence over other
> consequences.
>
>
>
> Any thoughts on if this could be added to the development for the next
> release cycle?
>
> Thanks for all of your help!
>
>
>
> Andrew R. Carson, Ph.D.
>
>
>
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