<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>
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