[ensembl-dev] Clarifying VEP outputs for inframe insertions

[Will McLaren]

Hi John,

In Ensembl coordinates an insertion is described as falling between two
coordinates, so the example in two APTP is inserted between 271 and 272.
This will be the case for an input variant that is an insertion (see the
section about insertions here
http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#input)

In the first example, while this resolves to an inframe insertion,
presumably the input variant type is not an insertion but rather an MNP
where the ALT sequence is longer than the REF.

It might be clearer (or I might be able to provide a clearer explanation at
least!) if you could provide the input variants that give rise to these two
cases.

Regards

Will McLaren
Ensembl Variation

On 29 September 2016 at 19:14, John M.C. Ma <manchunjohn-ma at uiowa.edu>
wrote:

> Hi,
>
> I'm reviewing my VEP output from VEP 84 for parsing scripts. I'm
> confused regarding the inconsistent annotations for inframe
> insertions.
>
> I have encountered, in the output from a single VEP run, two ways how
> VEP notates protein-level changes. For your convenience, the fields
> names used here are the same ones used in CSQ outputs.
>
> 1. The first type would have only a single number in the
> Protein_position field, and the Animo_acids field would include the
> residue immediately before the insertion. For example,
> Protein_position = 114, Animo_acids=A/AILH.
>
> 2. The second type includes two numbers in the Protein_position field,
> and in the Anime_acids field the ref AA is marked as -. For example,
> Protein_position=271-272, Animo_acids=-/APTP.
>
> While I have an ides about how to parse these two types, I'm puzzled
> about this inconsistency.
>
> For your reference, I was running with local e84 GRCm38 cache with
> fasta file with VEP 84 and perl 5.22.1 in an Linux environment.
>
> Thanks for the assistance.
>
> Cheers,
>
> John
>
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