[ensembl-dev] Bug Report on TranscriptVariationAllele.pm line 702

Sarah Hunt seh at ebi.ac.uk
Fri Aug 31 10:18:03 BST 2012


Hi Duarte,

Thanks for reporting this one. I have been able to recreate the error
by inputing a variant for which the alt allele specified in the VCF
matched the reference sequence at the position given in the VCF and
the protein level change (considering the input alt and ref alleles)
was synonymous. This could happen if the VCF and ensembl annotation
used different genome assemblies.

I've checked an updated version of TranscriptVariationAllele.pm into
CVS which handles the error better. Do let me know if this does not
sort out the problem you are seeing.

Best wishes,

Sarah

On Thu, Aug 30, 2012 at 3:57 PM, Duarte Molha <Duarte.Molha at ogt.co.uk> wrote:
> I came across this warning message when running a mouse genome vcf file with
> the --hgvs flag present
>
>
>
> Use of uninitialized value in concatenation (.) or string at
> /Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 702.
>
>
>
> I believe you had a similar bug on TranscriptVariationAllele.pm in VEP 2.5
> that got corrected. Maybe there was some sort of regression in the perl API
> for v2.6?
>
>
>
> Best Regards
>
>
>
> Duarte Molha
>
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe):
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>




More information about the Dev mailing list