[ensembl-dev] VEP - Reference contig not present

[Hans Vasquez-Gross]

Hello,

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.

UCW_Kronos_U_deg7180000303158   201     Kronos387       C       T       40
     Pass    seed_avail=Kronos387;CSQ=T||||intergenic_variant||||||||
UCW_Kronos_U_deg7180000303161   92      Kronos571       G       A       40
     Pass    seed_avail=Kronos571;CSQ=A||||intergenic_variant||||||||
UCW_Kronos_U_deg7180000303185   180     Kronos433       G       A       40
     Pass    seed_avail=Kronos433;CSQ=A||||intergenic_variant||||||||
UCW_Kronos_U_deg7180000303219   113     Kronos572       C       T       40
     Pass    seed_avail=Kronos572;CSQ=T||||intergenic_variant||||||||
UCW_Kronos_U_deg7180000303219   118     Kronos533       T       T       40
     Pass    seed_avail=Kronos533
UCW_Kronos_U_deg7180000303219   134     Kronos433       A       A       40
     Pass    seed_avail=Kronos433
UCW_Kronos_U_deg7180000303219   151     Kronos382       T       T       40
     Pass    seed_avail=Kronos382


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.

Any ideas why some of these contigs not present in the reference are
getting labeled with CSQ but others are not?

Cheers,
-Hans
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