[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
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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