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Hi Oliver,<br>
<br>
Thanks for reporting this one. There was an issue in identifying the
peptides surrounding inframe insertions just before the stop codon.
The impact was an HGVSp string like
ENSP00000319417.5:p.412_413insCysLysArgPhe being produced rather
than the more useful
ENSP00000319417.5:p.Asn412_Ter413insCysLysArgPhe. There is a fix for
this in branch 78 now, if you would like to pick it up from Github.<br>
<br>
It's good to hear you are enjoying VEP!<br>
<br>
Best wishes,<br>
<br>
Sarah<br>
<br>
<div class="moz-cite-prefix">On 29/01/2015 21:47, Homann, Oliver
wrote:<br>
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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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