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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>
</blockquote>
<br>
Regards,<br>
Guillermo.<br>
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