[ensembl-dev] No consequence for variant

[Will McLaren]

Hi again,

Thanks for that - it was the JSON output that was the issue.

I've patched a fix to ensembl-variation on release/83 - if you re-run
INSTALL.pl or do a git pull in ensembl-variation (if you used git) you
should get the fix.

Thanks again,

Will

On 9 February 2016 at 11:21, Sebastian Ginzel <sginze2s at inf.h-brs.de> wrote:

> Hi,
>
> I am using json output format.
>
> The command line is:
>
> perl /path/to/vep/variant_effect_predictor.pl \
> -i /tmp/vep_failed2.vcf \
> -o /tmp/vep_annots.json \
> --offline \
> --cache \
> --dir /path/to/vep/cache \
> --json \
> --force_overwrite \
> --quiet \
> --no_progress \
> --species=homo_sapiens \
> --buffer_size 5000 \
> --fork 2 \
> --regulatory \
> --merged \
> --ccds \
> --uniprot \
> --hgvs \
> --symbol \
> --numbers \
> --domains \
> --canonical \
> --protein \
> --biotype \
> --uniprot \
> --tsl \
> --appris \
> --gene_phenotype \
> --gmaf \
> --maf_1kg \
> --maf_esp \
> --maf_exac \
> --pubmed \
> --variant_class \
> --no_stats \
> --dont_skip \
> --sift b \
> --polyphen b
>
> Error message is:
> Can't call method "rank" on an undefined value at
> /path/to/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1975
>
> Regards,
> Sebastian
>
>
> Am 09.02.2016 um 11:34 schrieb 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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>
>
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