[ensembl-dev] "subseq" error

[Will McLaren]

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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