[ensembl-dev] VEP warnings after finish

[Sarah Hunt]

Hi Guillermo,

Thanks - that's good to know. This means one transcript-variant 
combination is failing the HGVS annotation. We are aware of problems 
with the mapping of a few RefSeq transcripts to the genome, so I suspect 
this is the cause of the message. It is possible that the 
transcript-variant combination would fail a check for required data and 
not be present in the output at all, but if it is the HGVS transcript 
level annotation will be malformed. We'll add checks to skip such 
incompatible cases in future.

Sarah

On 19/10/2016 07:46, Guillermo Marco Puche wrote:
>
> Hi Sarah,
>
> I'm only seeing the warnings mentioned in my previous message. All at 
> once a the end of the VEP execution of 415372 variants. Yes I'm using 
> RefSeq. With mangled HGVS do you refer to a malformed HGVS information 
> field?
>
> Regards,
> Guillermo.
>
>
> On 10/18/2016 06:15 PM, Sarah Hunt wrote:
>>
>>
>> Hi Guillermo,
>>
>> These messages suggest an inconsistency in the way the variant is 
>> mapping to the transcript, or the way the transcript is mapping to 
>> the genome. Each warning mentioning 'TranscriptVariationAllele.pm 
>> line 703' is from a different variant-transcript pairing and is 
>> probably resulting in a HGVS c or n string without a start location, 
>> assuming consequences can be called.
>>
>> How many mentions of 'TranscriptVariationAllele.pm line 703' are you 
>> seeing? Are you using RefSeq? If you notice any mangled HGVS, the 
>> examples would be very useful in tracking down the specific issue, 
>> but we can definitely add further checks to ensure all required 
>> information is available before HGVS annotation starts.
>>
>> Best wishes,
>>
>> Sarah
>>
>> On 18/10/2016 14:47, Guillermo Marco Puche wrote:
>>>
>>> Dear devs,
>>>
>>> I'm getting a lot of warnings when annotating a big VCF file. VEP 
>>> annotation seems to write a correctly annotated VCF however I'm 
>>> getting a lot of "TranscriptVariationAllele.pm" warnings. Any idea 
>>> what could be causing this issue?
>>>
>>>     2016-10-18 14:53:38 - Writing output
>>>     2016-10-18 14:53:38 - Processed 415372 total variants (26
>>>     vars/sec, 35 vars/sec total)
>>>     2016-10-18 14:53:38 - Finished!
>>>     Use of uninitialized value $cdna_position in pattern match (m//)
>>>     at
>>>     /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>>>     line 1901.
>>>     Use of uninitialized value $cdna_coord in concatenation (.) or
>>>     string at
>>>     /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>>>     line 1933.
>>>     Use of uninitialized value $exon_start_coord in addition (+) at
>>>     /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>>>     line 703.
>>>     Use of uninitialized value $cdna_position in pattern match (m//)
>>>     at
>>>     /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>>>     line 1901.
>>>     Use of uninitialized value $cdna_coord in numeric gt (>) at
>>>     /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>>>     line 1907.
>>>     Use of uninitialized value $cdna_coord in string eq at
>>>     /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>>>     line 1913.
>>>     Use of uninitialized value $cdna_coord in pattern match (m//) at
>>>     /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>>>     line 1921.
>>>     Use of uninitialized value $cdna_coord in numeric ge (>=) at
>>>     /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>>>     line 1924.
>>>
>>>
>>> Regards,
>>> Guillermo.
>>>
>>>
>>>
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>>
>>
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