[ensembl-dev] VEP - TranscriptVariationAllele.pm errors

Sarah Hunt seh at ebi.ac.uk
Wed May 8 15:40:55 BST 2013


Thanks Stuart - that's really useful.

Slashes are the required allele delimiter - the input with a comma is being
treated as biallelelic, with the alt allele as "-,A" which the HGVS
jiggerypokkery code refuses to deal with at all.

The variant coordinates aren't logically compatible with the allele options
which is why it's complaining - G/A looks like a substitution, but the
coordinates look like a frameshift. We can probably make it handle this
sort of thing a little more gracefully, but I wouldn't trust such inputs.


Looking at the dbSNP record:

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs55927445

it looks as if 2 neighbouring indels have been merged, suggesting this may
not be the most reliable of variants.


Sarah


On Wed, May 8, 2013 at 2:57 PM, Stuart Meacham <sm766 at cam.ac.uk> wrote:

> Hi
>
> Thanks for the reply, it seems that my source alternate allele(s) had
> slashes ('/') instead of commas (',') which were ok for the VEP but not for
> the TranscriptVariationAllele.pm when doing it's HGVS jiggerypokkery!
>
> eg:
>
> X       2726228 2726230 G/-,A   +       rs55927445
>
> is fine
>
> X       2726228 2726230 G/-/A   +       rs55927445
>
> is not
>
> even though this is how it is displayed in ensembl @
> http://www.ensembl.org/Homo_**sapiens/Variation/Summary?r=X:**
> 2725728-2726728;source=dbSNP;**v=rs55927445;vdb=variation;vf=**12794020<http://www.ensembl.org/Homo_sapiens/Variation/Summary?r=X:2725728-2726728;source=dbSNP;v=rs55927445;vdb=variation;vf=12794020>
>
> Thanks
>
> Stuart
>
>
> On 08/05/13 13:09, Sarah Hunt wrote:
>
>> Hi Stuart,
>> Hope all goes well with you! Do you have any input you can share to help
>> debug this one?
>> Sarah
>>
>>  On Wed, May 8, 2013 at 12:02 PM, Stuart Meacham <sm766 at cam.ac.uk<mailto:
>> sm766 at cam.ac.uk>> wrote:
>>
>>     Hi,
>>
>>     When using the VEP (Ensembl 71) with apparently well formed data I
>>     am getting some errors generated by the above mentioned module. It
>>     appears $hgvs_notation->{type} is queried when not defined at
>>     several locations in the module. I am using the 'ensembl' data
>>     format as input and outputting a vcf with the --everything flag.
>>     The VEP is producing output for all 715 records provided. The
>>     errors are for locations on ch1 and chrX.
>>
>>     For reference:
>>
>>     Use of uninitialized value in string eq at
>>     /home/sm766/src/vep/variant_**effect_predictor/Bio/EnsEMBL/**
>> Variation/**TranscriptVariationAllele.pm
>>     line 934.
>>     Use of uninitialized value in string eq at
>>     /home/sm766/src/vep/variant_**effect_predictor/Bio/EnsEMBL/**
>> Variation/**TranscriptVariationAllele.pm
>>     line 938.
>>     Use of uninitialized value in string eq at
>>     /home/sm766/src/vep/variant_**effect_predictor/Bio/EnsEMBL/**
>> Variation/**TranscriptVariationAllele.pm
>>     line 976.
>>     Use of uninitialized value in string eq at
>>     /home/sm766/src/vep/variant_**effect_predictor/Bio/EnsEMBL/**
>> Variation/**TranscriptVariationAllele.pm
>>     line 984.
>>     Use of uninitialized value in string eq at
>>     /home/sm766/src/vep/variant_**effect_predictor/Bio/EnsEMBL/**
>> Variation/**TranscriptVariationAllele.pm
>>     line 753.
>>     Use of uninitialized value in string eq at
>>     /home/sm766/src/vep/variant_**effect_predictor/Bio/EnsEMBL/**
>> Variation/**TranscriptVariationAllele.pm
>>     line 769.
>>     Use of uninitialized value in string eq at
>>     /home/sm766/src/vep/variant_**effect_predictor/Bio/EnsEMBL/**
>> Variation/**TranscriptVariationAllele.pm
>>     line 775.
>>     Use of uninitialized value in string eq at
>>     /home/sm766/src/vep/variant_**effect_predictor/Bio/EnsEMBL/**
>> Variation/**TranscriptVariationAllele.pm
>>     line 775.
>>     Use of uninitialized value in string eq at
>>     /home/sm766/src/vep/variant_**effect_predictor/Bio/EnsEMBL/**
>> Variation/**TranscriptVariationAllele.pm
>>     line 806.
>>     Use of uninitialized value in string eq at
>>     /home/sm766/src/vep/variant_**effect_predictor/Bio/EnsEMBL/**
>> Variation/**TranscriptVariationAllele.pm
>>     line 825.
>>
>>     Thanks
>>
>>     Stuart
>>
>>
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