[ensembl-dev] No consequence for variant

Sebastian Ginzel sginze2s at inf.h-brs.de
Wed Feb 3 14:07:21 GMT 2016

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 

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 

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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