[ensembl-dev] VEP warnings after finish

[Sarah Hunt]

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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