[ensembl-dev] vep --pick option

Will McLaren wm2 at ebi.ac.uk
Tue May 6 09:14:25 BST 2014


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


On 5 May 2014 23:12, Allison Regier <aregier at genome.wustl.edu> wrote:

> I noticed that with the --pick option, vep will only annotate one
> alternate allele if there are multiple alternates in the vcf entry.  This
> seems undesirable - is it intended?
> For example, a variant at
> 21      39207700        .       T       C,G
>
> got the annotation
>
> CSQ=C|ENSG00000157542|ENST00000609713|Transcript|INTRONIC||||||||||||-1|YES|KCNJ6|HGNC|||ENST00000609713.1:c.25+5260A>G|
> with --pick turned on
>
> and
>
> CSQ=C|ENSG00000157542|ENST00000288309|Transcript|INTRONIC||||||||-1|KCNJ6|HGNC|,G|ENSG00000157542|ENST00000288309|Transcript|INTRONIC||||||||-1|KCNJ6|HGNC|,C|ENSG00000157542|ENST00000609713|Transcript|INTRONIC||||||||-1|KCNJ6|HGNC|,G|ENSG00000157542|ENST00000609713|Transcript|INTRONIC||||||||-1|KCNJ6|HGNC|
> with --pick turned off
>
> I would have liked to see the “top” transcript picked for each alternate
> allele:
>
> CSQ=C|ENSG00000157542|ENST00000609713|Transcript|INTRONIC||||||||||||-1|YES|KCNJ6|HGNC|||ENST00000609713.1:c.25+5260A>G|,G|ENSG00000157542|ENST00000609713|Transcript|INTRONIC||||||||-1|KCNJ6|HGNC|
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