[ensembl-dev] VEP - TranscriptVariationAllele.pm errors

[Stuart Meacham]

Hi,

When using the VEP (Ensembl 71) with apparently well formed data I am 
getting some errors generated by the above mentioned module. It appears 
$hgvs_notation->{type} is queried when not defined at several locations 
in the module. I am using the 'ensembl' data format as input and 
outputting a vcf with the --everything flag. The VEP is producing output 
for all 715 records provided. The errors are for locations on ch1 and chrX.

For reference:

Use of uninitialized value in string eq at 
/home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm 
line 934.
Use of uninitialized value in string eq at 
/home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm 
line 938.
Use of uninitialized value in string eq at 
/home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm 
line 976.
Use of uninitialized value in string eq at 
/home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm 
line 984.
Use of uninitialized value in string eq at 
/home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm 
line 753.
Use of uninitialized value in string eq at 
/home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm 
line 769.
Use of uninitialized value in string eq at 
/home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm 
line 775.
Use of uninitialized value in string eq at 
/home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm 
line 775.
Use of uninitialized value in string eq at 
/home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm 
line 806.
Use of uninitialized value in string eq at 
/home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm 
line 825.

Thanks

Stuart