[ensembl-dev] [VEP] Bug stripping REF/ALT alleles ?

João Eiras joao.eiras at gmail.com
Fri Jul 14 12:27:54 BST 2017


On 14 July 2017 at 12:15, William McLaren <wm2 at ebi.ac.uk> wrote:
> Hi João,
>
> VEP trims alleles if the substitution is unbalanced (typically an insertion
> or deletion where the length(REF) != length(ALT)), and by default only trims
> the first base from each.
>
> You may force VEP to fully strip each pair of alleles using --minimal [1];
> using this flag I get missense as expected.
>
> We’re currently working on expanding and clarifying the documentation for
> this, with the update available in release 90.
>
> Regards
>

Hi William.

Indeed that option fixes the annotation, but it breaks other things.
I'm parsing the JSON output and using the variant_allele property to
match an annotation with the input allele. But variant_allele is
missing in deletes so the match cannot happen. But meanwhile I managed
to get the code working with "codons".

I think the minimal option shouldn't be there as it breaks deletes
awfully. For instance, how to strip "chr1 99772782 ACTG ACT,ATG,ACG"?
The alt will always be empty.

I also think that VEP should do the stripping internally always when
producing the annotation. Whether minimal is present or not should
have no influence in the annotation.

Thank you for your time !



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