[ensembl-dev] No consequence for variant

[Sebastian Ginzel]

Hi Will,

thanks for your explanation.

Do you have any suggestion how to filter these variants before processing?
Because VEP fails and stops annotating the rest of the VCF.


Regards,
Sebastian

> Hi Sebastian,
>
> In some cases when using the RefSeq transcript cache, the mappings we are
> provided by NCBI for a particular transcript may cause issues.
>
> In this case our database contains duplicate entries for NM_001271893.1,
> one of which is marked as a protein coding transcript but has no defined
> CDS. Your variant overlaps this duplicate, and because of the conflicting
> definition the VEP doesn't know what to call the variant and a warning is
> given on STDERR and in the warnings file.
>
> I would consider it safe to filter out or ignore any cases where we are
> unable to assign a consequence type such as this as they typically
> correspond to transcript annotations that are faulty to begin with.
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
> On 3 February 2016 at 14:07, Sebastian Ginzel <sginze2s at inf.h-brs.de> wrote:
>
>> Hi Ensembl,
>>
>> I am trying to annotate a variant using VEP v83 with the
>> homo_sapiens_merged cache.
>>
>> When I reach this variant in my VCF file:
>> 2    239832097    .    A    T    100    PASS    .    .    .
>>
>> VEP fails with:
>> Can't call method "rank" on an undefined value at
>> /path/to/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1975
>>
>> The function vf_to_consequnces returns '?' as a consequence for this
>> variant.
>>
>> I have taken the liberty to attach the Data::Dumper output for a couple of
>> relevant variables as well as the parameters used to call the VEP script.
>>
>> When looking at the result of vf_to_consequences it seems that the Codons
>> and Amino_acids fields are undefined (line 98 & 100), although the variant
>> is predicted protein_coding (line 85).
>>
>> I got the same error for variants up- and downstream of that location.
>>
>> Can anyone confirm this? And if so: has an idea on how to fix it?
>>
>>
>> Best wishes,
>> Sebastian Ginzel
>>
>>
>>
>>
>>
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