[ensembl-dev] "subseq" error

[S Venkata Suresh Kumar]

Thanks. I will be looking forward till all the consequences are
incorporated in HGVS syntax.

However, VEP it self is very useful tool so far for us.

regards
vs
On 02/29/2012 03:10 PM, Will McLaren wrote:
> Hello again,
>
> Currently the HGVS parser only works reliably with a limited subset of
> the HGVS nomenclature types. The 'ins' type is not currently
> supported.
>
> Furthermore, when using --refseq only coding HGVS notations can be
> parsed - we don't store the chromosomes as you have supplied here
> (e.g. NC_000021.8:g.36421412_36421413insA).
>
> You could, however, easily just use the chromosome name and not use
> --refseq here e.g.
>
> 21:g.36421412_36421413insA
>
> however, this unfortunately will still not work as we cannot yet parse
> the 'ins' type. Other basic types should work correctly, however, and
> we will work on getting the other types supported in future.
>
> However, I am still surprised that the script does not fail gracefully
> - when I try this I get the error:
>
> WARNING: Unable to parse HGVS notation 'NC_000021.8:g.36421412_36421413insA'
> The variant class for HGVS notation
> 'NC_000021.8:g.36421412_36421413insA' is unknown or could not be
> correctly recognized at
> ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm
>
> Thanks
>
> Will
>
> On 29 February 2012 08:06, S Venkata Suresh Kumar
> <suresh.surampudi at india.semanticbits.com> wrote:
>> 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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