[ensembl-dev] VEP - Reference contig not present

[Will McLaren]

Hi Hans,

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.

Beyond this, I am not exactly sure what the issue is without some more
information:

What species are you analysing?

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?

Regards

Will McLaren
Ensembl Variation


On 21 August 2014 20:08, Hans Vasquez-Gross <havasquezgross at ucdavis.edu>
wrote:

> 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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