[ensembl-dev] VEP warnings after finish

[Guillermo Marco Puche]

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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