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

[Andrew Carson]

Thank you very much Dr. McLaren.
Just one clarification to the LRG choice. Is the LRG always presented as the first consequence (if it exists)? If this is true, then if the --pick chooses the worst consequence, and there are multiple transcripts with the same "worst consequence", does VEP --pick the first transcript with that consequence? If that is true, if the LRG contains the "worst consequence" along with other similar transcripts, will --pick successfully choose this consequence over other equal transcripts?

Any help on this would be appreciated.
Thank you again!
Andrew

>I should also say that there's currently no way to prioritise LRG
>consequences other than filtering using filter_vep.pl, though this wouldn't
>be a complete solution.
>
>Will
>
>
>On 1 April 2014 09:51, Will McLaren <wm2 at ebi.ac.uk<http://lists.ensembl.org/mailman/listinfo/dev>> wrote:
>
> 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<http://lists.ensembl.org/mailman/listinfo/dev>> 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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