[ensembl-dev] "subseq" error

[S Venkata Suresh Kumar]

I am using a file (without header) with one HGVS syntax :
NC_000021.8:g.36421412_36421413insA

I am trying to convert this into VCF (to test vep script). Following is
the way I am trying:

$ perl /opt/vep/variant_effect_predictor.pl -i hgvs -o hgvs.vcf -refseq
-convert vcf --verbose -force

Regards
vs
On 02/28/2012 10:55 PM, Will McLaren wrote:
> Hello,
>
> Are you able to provide an example of the line that is causing this issue?
>
> Thanks
>
> Will McLaren
> Ensembl Variation
>
> On 28 February 2012 11:13, S Venkata Suresh Kumar
> <suresh.surampudi at india.semanticbits.com> wrote:
>> Hi All
>>
>> When i am trying to convert a hgvs file to vcf file, I am getting
>> following error:
>>
>> "Can't call method "subseq" on an undefined value at
>> /opt/vep/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm
>> line 1272, <GEN0> line 1."
>>
>> any clues ?
>>
>> I am using vep 2.4, OS linux, bioperl 1.6.901-2.
>>
>> regards
>> vs
>>
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