[ensembl-dev] No consequence for variant

[Will McLaren]

Hi Sebastian,

The script shouldn't die in this situation - which output format are you
using? It would be useful if you could share the exact command you are
using.

Will

On 9 February 2016 at 10:22, Sebastian Ginzel <sginze2s at inf.h-brs.de> wrote:

> 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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> >>
>
>
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