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<p class="MsoNormal">Hello,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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):<o:p></o:p></p>
<p class="MsoNormal"> “Use of uninitialized value in string eq at /<mypath>/ensembl-tools-release-78/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1220”<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Here are the offending lines in the perl module:<o:p></o:p></p>
<p class="MsoNormal"> 1219 ### Convert peptide to 3 letter code as used in HGVS<o:p></o:p></p>
<p class="MsoNormal"> 1220 unless( $hgvs_notation->{ref} eq "-"){<o:p></o:p></p>
<p class="MsoNormal"> 1221 $hgvs_notation->{ref} = Bio::SeqUtils->seq3(Bio::PrimarySeq->new(-seq => $hgvs_notation->{ref}, -id => 'ref', -alphabet => 'protein')) || "";<o:p></o:p></p>
<p class="MsoNormal"> 1222 }<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I tracked down one of the offending entries, but it isn’t immediately obvious to me why it is causing an error:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT MySample<o:p></o:p></p>
<p class="MsoNormal">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<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any ideas what the problem might be?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal">Oliver Homann<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">P.S. Apart from this small glitch, VEP is teriffic!<o:p></o:p></p>
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