[ensembl-dev] Error msg in VEP using HGVS option

Duarte Molha Duarte.Molha at ogt.com
Mon Nov 11 15:57:42 GMT 2013


Dear Developers

On the documentation, you indicate that you can use the option HGVS but that it will need a valid connection to the database.
However when I try to use it I get this error message:

substr outside of string at /NGS_Tools/ensembl-latest/ensembl-variation/modules//Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1218.
Use of uninitialized value $test_seq in string eq at /NGS_Tools/ensembl-latest/ensembl-variation/modules//Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1220.

If I supply a fasta file then I do not get this error. Is the FASTA file always required for HGVS? From the documentation I got the understanding that the fasta file was only required if operating in offline mode.

Best regards

Duarte Molha

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