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<p>Hi Guillermo,</p>
<p>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.<br>
</p>
Sarah<br>
<br>
<div class="moz-cite-prefix">On 19/10/2016 07:46, Guillermo Marco
Puche wrote:<br>
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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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