<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi,<div class=""><br class=""></div><span class="">Thank you for this issue report. I’ve taken a look over the last couple of days, and it’s definitely a bug. When VEP looks for the sequences flanking the variant, it takes a chunk of 100 bases at either side, and it doesn’t expand correctly if the indel covers a larger area then that. So for example, 17:g.16029315_16029366del shifts correctly, while 17:g.16029315_16029421del does not.<br class=""></span><span class=""><br class=""></span><div class="">We’re currently making significant improvements to our HGVS 3’ shifting code, which will resolve this issue, however this is currently scheduled for release in March 2019.</div><div class=""><br class=""></div><div class="">Thanks for reporting this one, and if there’s anything else we can do to help please let us know.</div><div class=""><br class=""></div><div class="">Kind Regards,</div><div class="">Andrew</div><div class=""><br class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 28 Nov 2018, at 10:13, Bhavana Harsha <<a href="mailto:bh4@sanger.ac.uk" class="">bh4@sanger.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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Hello,
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<div class="">We’ve come across something strange in VEP.</div>
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<div class="">For the GRCh37 variant 17:g.16029315_16029421del, VEP returns the following transcript annotation:</div>
<div class="">HGVSg: 17:g.16029316_16029422del</div>
<div class="">HGVSc: ENST00000395851.1:c.1609_1634+81del</div>
<div class="">HGVSc-offset = 0</div>
<div class="">HGVSg-offset = 1</div>
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<div class="">When we lift-over the genomic variant to GRCh38 (using the Ensembl API) and run VEP we get the following annotation for the same transcript:</div>
<div class="">Input: 17:g.16126002_16126108del</div>
<div class="">HGVSg: 17:g.16126003_16126109del<br class="">
HGVSc: ENST00000395851.5:c.1609_1634+81del<br class="">
HGVSc-offset = -1<br class="">
HGVSg-offset = 1</div>
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<div class="">Why does it shift the genomic syntax by 1 position in both the assemblies? </div>
<div class="">Shouldn’t GRCh37 VEP have shifted it by 2 bases or have I missed something here?</div>
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<div class="">We’re on campus and I’m happy to meet to explain this further, if needed.</div>
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<div class="">Regards,</div>
<div class="">Bhavana</div>
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Bhavana Harsha<br class="">
Senior Bioinformatician<br class="">
COSMIC<br class="">
Wellcome Trust Sanger Institute<br class="">
Hinxton, UK<br class="">
CB10 1SA<br class="">
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