[ensembl-dev] VEP - TranscriptVariationAllele.pm errors

[Sarah Hunt]

Hi Stuart,

TranscriptVariationAllele.pm is updated in CVS branch 71 to not complain
when the input is inconsistent like this example.

If you wanted to check your input for such problems the --check_ref option
compares the reference allele expected from the coordinates to that
supplied and warns of inconsistencies. Of course, it is slower to run VEP
with this option.
Thanks for reporting this.

All the best,

Sarah
On Wed, May 8, 2013 at 3:40 PM, Sarah Hunt <seh at ebi.ac.uk> wrote:

>
> 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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>>
>>
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