[ensembl-dev] No consequence for variant

[Sebastian Ginzel]

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 
> <mailto: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 atinf.h-brs.de <http://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
>     >>
>     >>
>     >>
>     >>
>     >>
>     >> _______________________________________________
>     >> Dev mailing list    Dev atensembl.org <http://ensembl.org>>> Posting guidelines and
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>     http://lists.ensembl.org/mailman/listinfo/dev >> Ensembl Blog:
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>
>
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#----------------------------------#
# ENSEMBL VARIANT EFFECT PREDICTOR #
#----------------------------------#

version 83

By Will McLaren (wm2 at ebi.ac.uk)

Configuration options:

appris             1
biotype            1
buffer_size        1
cache              1
canonical          1
ccds               1
core_type          core
dir                /path/to/cache
dir_plugins        /path/to/cache/Plugins
domains            1
dont_skip          1
force_overwrite    1
fork               2
gene_phenotype     1
gmaf               1
hgvs               1
host               ensembldb.ensembl.org
input_file         /tmp/vep_failed2.vcf
json               1
maf_1kg            1
maf_esp            1
maf_exac           1
merged             1
no_progress        1
no_stats           1
numbers            1
offline            1
output_file        /tmp/vep_annots.vcf
polyphen           b
port               3306
protein            1
pubmed             1
regulatory         1
rest               1
sift               b
species            homo_sapiens
stats              HASH(0x4b76300)
symbol             1
tsl                1
uniprot            1
variant_class      1
verbose            1

--------------------