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

[William McLaren]

On 15 July 2017 at 01:25:30, João Eiras (joao.eiras at gmail.com) wrote:

On 14 July 2017 at 15:38, William McLaren <wm2 at ebi.ac.uk> wrote:
> As the documentation for -minimal mentions you should use -allele_number to
> track alleles from input to output.
>

Can I suggest --minimal implying --allele_num ? Or rather, I think
allele_num should always be enabled since it's much more reliable that
trying to parse "variant_allele" or "codons"


Agreed; -minimal will switch on -allele_number in release/90.





> As you note for your example the ALT will be “-“ in all cases, but the
> start/end coordinates used to calculate the consequences will be different.
>
> It’s a matter of opinion unfortunately whether -minimal should be the
> default or not; we err on the side of trying not to confuse users too much
> by making it not the default. It’s something that could be up for
> consideration for change in the future, though.

That's fine by me, and I do think the output should resemble the input
as much as possible.

However, stripping the ref or not should NOT affect the result of the
annotation.
Agreed again, but unfortunately this is not as straightforward in practice as it sounds in principle.

It is something we’re working on for the future.

Regards

Will



Thank you so much for your time !
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