<div dir="ltr">Hi Hans,<div><br></div><div>You have some entries in your VCF where the ALT allele is the same as the REF allele; these are not considered variants by the VEP and hence won't be analysed.</div><div><br></div>
<div>Beyond this, I am not exactly sure what the issue is without some more information:</div><div><br></div><div>What species are you analysing?</div><div><br></div><div>You say you have supplemented the main reference from Ensembl with some other contigs - what exactly do you mean by this? Have you created entries in an Ensembl core database for these contigs with appropriate transcript info, or perhaps created your own VEP cache file from a GTF and FASTA file?</div>
<div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 21 August 2014 20:08, Hans Vasquez-Gross <span dir="ltr"><<a href="mailto:havasquezgross@ucdavis.edu" target="_blank">havasquezgross@ucdavis.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div dir="ltr"><div>Hello,</div><div><br></div><div>Recently, I ran VEP on a new VCF file based on release 22. We supplemented the main reference from Ensembl with some other contigs. Running VEP on this new VCF with the supplemental contigs, I get CSQ predictions for some contigs, but not others. </div>
<div><br></div><div><font face="courier new, monospace">UCW_Kronos_U_deg7180000303158 201 Kronos387 C T 40 Pass seed_avail=Kronos387;CSQ=T||||intergenic_variant||||||||</font></div><div><font face="courier new, monospace">UCW_Kronos_U_deg7180000303161 92 Kronos571 G A 40 Pass seed_avail=Kronos571;CSQ=A||||intergenic_variant||||||||</font></div>
<div><font face="courier new, monospace">UCW_Kronos_U_deg7180000303185 180 Kronos433 G A 40 Pass seed_avail=Kronos433;CSQ=A||||intergenic_variant||||||||</font></div><div><font face="courier new, monospace">UCW_Kronos_U_deg7180000303219 113 Kronos572 C T 40 Pass seed_avail=Kronos572;CSQ=T||||intergenic_variant||||||||</font></div>
<div><font face="courier new, monospace">UCW_Kronos_U_deg7180000303219 118 Kronos533 T T 40 Pass seed_avail=Kronos533</font></div><div><font face="courier new, monospace">UCW_Kronos_U_deg7180000303219 134 Kronos433 A A 40 Pass seed_avail=Kronos433</font></div>
<div><font face="courier new, monospace">UCW_Kronos_U_deg7180000303219 151 Kronos382 T T 40 Pass seed_avail=Kronos382 </font></div><div><br></div><div><br></div><div>I would have expected all of these entries to contain lines like the last 3 with no CSQ information, instead of the first ones with 'intergenic_variant' incorrectly labeled. </div>
<div><br></div><div>Any ideas why some of these contigs not present in the reference are getting labeled with CSQ but others are not?</div><div><br></div><div>Cheers,</div><div>-Hans</div></div>
</div>
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