<div dir="ltr"><div class="gmail_quote"><div dir="ltr">Hi,<div><br></div><div>I am trying to annotate a list of mutations in coding HGVS notation with VEP, most of them go through pretty ok, but some are creating troubles. One example is <span style="color:rgb(51,51,51);font-family:"Luxi Sans",Helvetica,Arial,Geneva,sans-serif;font-size:12.8px">TP53:c.110_120delinsC, here's the job output: </span><a href="https://www.ensembl.org/Homo_sapiens/Tools/VEP/Results?tl=fbegKEYtZPdXtACp-9377859">https://www.ensembl.org/Homo_sapiens/Tools/VEP/Results?tl=fbegKEYtZPdXtACp-9377859</a></div><div><br></div><div>And that's the relevant part from the VCF:</div><div>17  7676249 TP53:c.110_120delinsC   CCATTGCTTGG     C       .       .</div><div><div><div><br></div><div>Whenever i try to use the generated VCF downstream, there are issues because sequence starting at 17:7676249 in GRCh38 isn't actually <b>C</b>CATTGCTTGG like in VEP-generated VCF. It is shorter: CATTGCTTGG, see that here:</div><div><a href="https://www.ensembl.org/Homo_sapiens/Location/View?r=17:7676249-7676259" target="_blank">https://www.ensembl.org/Homo_sapiens/Location/View?r=17:7676249-7676259</a><br></div><div><br></div><div>And so there's a reference mismatch. I am missing something obvious?</div><div><br></div><div>Cheers,</div><div>Oliver</div></div></div></div>
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