[ensembl-dev] VEP (ver78) TranscriptVariationAllele.pm unitialized value error with --hgvs enabled

[Homann, Oliver]

Hello,

I have been using the VEP to annotate a GATK-generated VCF containing indels from a WGS genotyping project, and have encountered a small number of entries that result in the following error (only when -hgvs is enabled):
    "Use of uninitialized value in string eq at /<mypath>/ensembl-tools-release-78/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1220"

Here are the offending lines in the perl module:
     1219   ### Convert peptide to 3 letter code as used in HGVS
     1220   unless( $hgvs_notation->{ref} eq "-"){
    1221       $hgvs_notation->{ref}  = Bio::SeqUtils->seq3(Bio::PrimarySeq->new(-seq => $hgvs_notation->{ref}, -id => 'ref',  -alphabet => 'protein')) || "";
     1222   }

I tracked down one of the offending entries, but it isn't immediately obvious to me why it is causing an error:

#CHROM             POS        ID            REF         ALT         QUAL    FILTER   INFO      FORMAT              MySample
13           21729289             .               T              TCAGTTTTCTTTGTTGCTGACATCTCGGATGTTCTGTCCATGTTTAAGGAACCTTTTA                118.19   .               AC=1;AF=5.556e-03;AN=180;BaseQRankSum=0.744;DP=2652;FS=3.538;GQ_MEAN=66.68;GQ_STDDEV=20.39;InbreedingCoeff=-0.0085;MLEAC=1;MLEAF=5.556e-03;MQ=60.00;MQ0=0;MQRankSum=0.609;NCC=0;QD=0.13;ReadPosRankSum=-1.220e-01;SOR=0.252    GT:AD:DP:GQ:PL              0/1:41,8:.:99:160,0,14558

Any ideas what the problem might be?

Thanks,
Oliver Homann

P.S.  Apart from this small glitch, VEP is teriffic!
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