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

[Will McLaren]

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> 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> 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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>
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