[ensembl-dev] Various errors with VEP

[Levine, Adam]

I seem to be getting a number of different errors when using the VEP Perl script with various VCF input files all generated by GATK.

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1. Use of uninitialized value in concatenation (.) or string src/ensemble-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 778, <GEN0> line 82338.

2. Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE K$/ at /src/ensemble-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1196, <GEN0> line 653.

3. Use of uninitialized value in length at /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 980, <GEN0> line 15939.

4. Use of uninitialized value in string eq /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 761, <GEN0> line 15939.

5. Use of uninitialized value in substitution (s///) at /src/ensemble-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 997, <GEN0> line 15939.

6. Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE K$/ at /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1196, <GEN0> line 653.
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I was wondering whether anyone might be able to help me work out what these errors are. For all of these except for error 6, the analyses still ran.

Thank you,

Adam

Adam P. Levine