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<p>Hi Sarah,</p>
<p>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?</p>
<p>Regards,<br>
Guillermo.<br>
</p>
<br>
<div class="moz-cite-prefix">On 10/18/2016 06:15 PM, Sarah Hunt
wrote:<br>
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<p>Hi Guillermo,</p>
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. <br>
<br>
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.<br>
<br>
Best wishes,<br>
<br>
Sarah<br>
<br>
<div class="moz-cite-prefix">On 18/10/2016 14:47, Guillermo Marco
Puche wrote:<br>
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<p>Dear devs,</p>
<p>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?<br>
</p>
<blockquote>2016-10-18 14:53:38 - Writing output<br>
2016-10-18 14:53:38 - Processed 415372 total variants (26
vars/sec, 35 vars/sec total)<br>
2016-10-18 14:53:38 - Finished!<br>
Use of uninitialized value $cdna_position in pattern match
(m//) at
/share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
line 1901.<br>
Use of uninitialized value $cdna_coord in concatenation (.) or
string at
/share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
line 1933.<br>
Use of uninitialized value $exon_start_coord in addition (+)
at
/share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
line 703.<br>
Use of uninitialized value $cdna_position in pattern match
(m//) at
/share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
line 1901.<br>
Use of uninitialized value $cdna_coord in numeric gt (>) at
/share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
line 1907.<br>
Use of uninitialized value $cdna_coord in string eq at
/share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
line 1913.<br>
Use of uninitialized value $cdna_coord in pattern match (m//)
at
/share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
line 1921.<br>
Use of uninitialized value $cdna_coord in numeric ge (>=)
at
/share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
line 1924.<br>
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<br>
Regards,<br>
Guillermo.<br>
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