<div dir="ltr">Hi Konrad,<div><br></div><div>This is an interesting case. The insertion in VCF notation starts at position <span style="font-size:13px">141459861. When the VEP converts this internally to Ensembl notation (see </span><a href="http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#vcf">http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#vcf</a>), it becomes an insertion between positions <span style="font-size:13px">141459861 and </span><span style="font-size:13px">141459862. </span><span style="font-size:13px">This is represented in the Ensembl convention with start=</span><span style="font-size:13px">141459862 and end=</span><span style="font-size:13px">141459861.</span></div><div><span style="font-size:13px"><br></span></div><div><span style="font-size:13px">The exon ends at position </span><span style="font-size:13px">141459861 and the following intron starts at </span><span style="font-size:13px">141459862. This means that the ALT sequence is inserted between these positions, meaning that it falls in neither the exon nor the intron according to the reference coordinates and the algorithm the API uses to determine the overlap.</span></div><div><span style="font-size:13px"><br></span></div><div><span style="font-size:13px">I've illustrated this (very badly) here </span><a href="http://www.ebi.ac.uk/~wm2/insertion.png">http://www.ebi.ac.uk/~wm2/insertion.png</a></div><div><br></div><div>I don't know what people would consider to be the right approach here. Possibly since depending on the sequence inserted, biologically the inserted sequence could "join" either the exon or intron, we should report that it falls in both? Happy to take feedback anyway.</div><div><br></div><div>Regards</div><div><br></div><div>Will</div><div><span style="font-size:13px"><br></span></div><div><span style="font-size:13px"><br></span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 4 December 2014 at 02:29, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">konradk@broadinstitute.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi dev team,<br>
<br>
I'm getting some strange behavior when using VEP to annotate certain indels. In particular, the EXON field doesn't get populated for some reason. See below: a SNP at the same position looks fine (exon 39/91), while an indel doesn't get the same annotation. Any ideas about this?<br>
<br>
Thanks!<br>
-Konrad<br>
<br>
2 141459861 . C A 2 VQSRTrancheINDEL99.50to99.90 AC=1;CSQ=A|ENSG00000168702|ENST00000389484|Transcript|stop_gained&splice_region_variant|7123|6151|2051|E/*|Gaa/Taa||1||-1|LRP1B|HGNC|6693|protein_coding|YES|CCDS2182.1|ENSP00000374135|LRP1B_HUMAN|Q8WY27_HUMAN&Q8WY26_HUMAN&Q580W7_HUMAN&Q53TB8_HUMAN&Q53S76_HUMAN&Q53S73_HUMAN&Q53S26_HUMAN&Q53RL0_HUMAN&Q53RG4_HUMAN&Q53RA0_HUMAN&Q53QP5_HUMAN&Q53QM8_HUMAN&Q4ZG53_HUMAN&Q4ZFV5_HUMAN|UPI00001B045B|||39/91||PROSITE_profiles:PS51120&SMART_domains:SM00135&Superfamily_domains:SSF63825|ENST00000389484.3:c.6151G>T|ENSP00000374135.3:p.Glu2051Ter|||||||||||||||POSITION:0.445724637681159|||HC<br>
2 141459861 . C CATAAGTATTTGAGT 363.89 VQSRTrancheINDEL99.50to99.90 AC=1;CSQ=ATAAGTATTTGAGT|ENSG00000168702|ENST00000389484|Transcript|frameshift_variant&splice_region_variant&feature_elongation|7122-7123|6150-6151|2050-2051|-/TQILX|-/ACTCAAATACTTAT||1||-1|LRP1B|HGNC|6693|protein_coding|YES|CCDS2182.1|ENSP00000374135|LRP1B_HUMAN|Q8WY27_HUMAN&Q8WY26_HUMAN&Q580W7_HUMAN&Q53TB8_HUMAN&Q53S76_HUMAN&Q53S73_HUMAN&Q53S26_HUMAN&Q53RL0_HUMAN&Q53RG4_HUMAN&Q53RA0_HUMAN&Q53QP5_HUMAN&Q53QM8_HUMAN&Q4ZG53_HUMAN&Q4ZFV5_HUMAN|UPI00001B045B|||||PROSITE_profiles:PS51120&SMART_domains:SM00135&Superfamily_domains:SSF63825|ENST00000389484.3:c.6151-1_6151insACTCAAATACTTAT|ENSP00000374135.3:p.Glu2051ThrfsTer19|||||||||||||||POSITION:0.445652173913043||EXON_INTRON_UNDEF|LC<br>
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</blockquote></div><br></div>