[ensembl-dev] VEP 86 GRCh38 - alt contig names not recognized

[Will McLaren]

Hi Alison,

Thanks for bringing this to our attention, there was a bug in the way VEP
was handling chromosome names beginning with "chr".

This should be fixed now in the release/86 branch of the ensembl-variation
module; if you used INSTALL.pl to set up your command-line VEP then you can
re-run this to pick up the changes.

Regards

Will McLaren
Ensembl Variation

On 21 November 2016 at 15:53, MEYNERT Alison <alison.meynert at igmm.ed.ac.uk>
wrote:

> I've been annotating some GRCh38 (hs38DH) VCFs with VEP 86, and it's
> working fine for the primary assembly, but I'm getting warnings on the alt
> contig names, e.g.
>
>
> WARNING: Chromosome Un_GL000218v1 not found in cache on line 3416412
>
> It looks like VEP is just chopping the 'chr' prefixes and not fully
> mapping the alt contig names to the Ensembl-style versions. Both the web
> interface and the standalone Perl script give the same results; however,
> interestingly, when I enter a variant like this into the web interface,
> e.g.
>
> chrUn_GL000218v1 160424 . C CTTT,CTTTT
>
> And run the "instant VEP", I get a result (see attached screenshot). If I
> fix the contig name manually to GL000218.1, I get full results.
>
> Cheers,
> Alison
>
> --
> Alison Meynert
> alison.meynert at igmm.ed.ac.uk
>
> MRC Human Genetics Unit
> MRC IGMM
> University of Edinburgh
> Western General Hospital
> Crewe Road, Edinburgh EH4 2XU
> United Kingdom
>
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