[ensembl-dev] Error msg in VEP using HGVS option

[Sarah Hunt]

Hi Duarte,

A FASTA file is not a requirement for HGVS. Could you supply an
example of a variant triggering this error message?

Thanks,

Sarah

On Mon, Nov 11, 2013 at 3:57 PM, Duarte Molha <Duarte.Molha at ogt.com> wrote:
> Dear Developers
>
>
>
> On the documentation, you indicate that you can use the option HGVS but that
> it will need a valid connection to the database.
>
> However when I try to use it I get this error message:
>
>
>
> substr outside of string at
> /NGS_Tools/ensembl-latest/ensembl-variation/modules//Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 1218.
>
> Use of uninitialized value $test_seq in string eq at
> /NGS_Tools/ensembl-latest/ensembl-variation/modules//Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 1220.
>
>
>
> If I supply a fasta file then I do not get this error. Is the FASTA file
> always required for HGVS? From the documentation I got the understanding
> that the fasta file was only required if operating in offline mode.
>
>
>
> Best regards
>
>
>
> Duarte Molha
>
>
>
>
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