[ensembl-dev] vep --pick option

[Allison Regier]

Yes, such an option would definitely be helpful because each individual may have a different combination of alternate alleles, and we may be interested in several of them.
As a workaround I will try splitting the vcf and recombining - but this needs to be done with care to make sure the alleles are still referenced correctly in the individual genotypes.
thank you!
-Allison

> Hello,
> 
> Yes, this is the intended behaviour. Most users who requested this feature
> were interested in one consequence per variant position.
> 
> I can possibly add another option (something like --pick_allele) that does
> this if there is enough demand.
> 
> You could also split your VCF entry across two lines with one per allele,
> this would give you the desired effect too.
> 
> Regards
> 
> Will McLaren
> Ensembl Variation
> 


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