<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">I get this error on some VCF files with the Variant Effect Predictor. It seems to be caused by an anomaly in the VariationFeature hgvs_notation code when an insert follows a stop codon (and maybe in other cases?).<div><br></div><div><div>substr outside of string at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/VariationFeature.pm line 1675, <GEN0> line 10050.</div><div>Use of uninitialized value in concatenation (.) or string at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/VariationFeature.pm line 1675, <GEN0> line 10050.</div><div><br></div><div>An example of a VCF input line is:</div><div>16<span class="Apple-tab-span" style="white-space:pre"> </span>84497336<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>T<span class="Apple-tab-span" style="white-space:pre"> </span>TAGTGGA<span class="Apple-tab-span" style="white-space:pre"> </span>6710.07<span class="Apple-tab-span" style="white-space:pre"> </span>InDel<span class="Apple-tab-span" style="white-space:pre"> </span>AC=1;AF=0.50;AN=2;BaseQRankSum=-7.179;DP=159;FS=2.028;GC=55.61;HRun=0;HaplotypeScore=765.4756;IndelType=INS.NumRepetitions_1.EventLength_6.;MQ=153.37;MQ0=0;MQ0Fraction=0.0000;MQRankSum=5.013;Num454=0;NumOther=0;NumSLX=159;NumSOLiD=0;QD=42.20;ReadPosRankSum=-0.390;SB=-3325.82;SBD=1.32<span class="Apple-tab-span" style="white-space:pre"> </span>GT:AD:DP:GQ:PL<span class="Apple-tab-span" style="white-space:pre"> </span>0/1:112,47:159:99:6710,0,4955</div><div><br></div><div>The code in VariationFeature.pm that throws the error is:</div><div><div><span class="Apple-tab-span" style="white-space:pre"> </span> $hgvs_notation->{'hgvs'} .= substr($hgvs_notation->{'ref'},0,3) . $hgvs_notation->{'start'} . '_' . substr($hgvs_notation->{'ref'},3,3) . $hgvs_notation->{'end'} . $hgvs_notation->{'type'} . $hgvs_notation->{'alt’};</div></div><div><br></div><div>In this example, $hgvs_notation->{'ref’} is ‘X’.</div><div><br></div><div>So substr($hgvs_notation->{'ref'},3,3) emits a warning and returns undef.</div><div><br></div><div>Apparently this situation arises because the termination codon is being represented as ‘X’ instead of the 3-letter ‘Ter’</div><div><div><span class="Apple-tab-span" style="white-space:pre"> </span># Replace termination codon code 'Ter' with the HGVS-preferred 'X'</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>$hgvs_notation->{'alt'} =~ s/Ter|\*/X/i;</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>$hgvs_notation->{'ref'} =~ s/Ter|\*/X/i;</div></div><div><br></div><div>Perhaps this is merely a case of an annoying warning the needs to be cleaned up. Possibly, also, something may end up missing in the HGVSp string. In my example, this string comes out as ENSP00000393378.2:p.X796_[?]797insTrpLysextX3 where nothing is at the position indicated by [?].</div><div><br></div><div>This example raises another question.</div><div><br></div><div>Is it correct to append “extX3” to the HGVSp string if what is going on here is an insert after the stop codon rather than a lost stop?</div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-family: Helvetica; font-size: 12px; "><p class="MsoNormal" style="font-family: 'Lucida Grande'; font-size: 10px; "><font class="Apple-style-span" face="'Devanagari MT'" size="7"><span class="Apple-style-span" style="font-size: 27px; "><font class="Apple-style-span" size="5"><span class="Apple-style-span" style="font-size: 18px; ">ॐ</span></font></span></font></p><p></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; line-height: 19px; font: normal normal normal 16px/normal Helvetica; "><span class="Apple-style-span" style="font-family: 'Lucida Grande'; font-size: 10px; ">Michael Yourshaw</span></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">UCLA Geffen School of Medicine</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Department of Human Genetics, Nelson Lab</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">695 Charles E Young Drive S</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Gonda 5554</span></div><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 3px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Los Angeles CA 90095-8348 USA</span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 3px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; color: rgb(0, 0, 153); "><span style="text-decoration: underline; letter-spacing: 0px; "><a href="mailto:myourshaw@ucla.edu">myourshaw@ucla.edu</a></span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">970.691.8299</span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; font: normal normal normal 9px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">This message is intended only for the use of the addressee and may contain information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY WORK PRODUCT. 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