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

[Will McLaren]

Hi Alison,

Those that remain have no relevant data mapped to them in Ensembl (either
transcripts or known variants), so we do not record them in the cache, e.g.

http://www.ensembl.org/Homo_sapiens/Location/View?r=KI270722.1:1-194050

VEP shouldn't really warn in these cases, and this will be fixed in a
future version.

Regards

Will McLaren
Ensembl Variation

On 5 December 2016 at 15:38, MEYNERT Alison <alison.meynert at igmm.ed.ac.uk>
wrote:

> Hi Will,
>
>
> Thanks, have just tested the update. Some of the contig names now work:
>
>
> chr11_KI270721v1
>
> chr14_GL000009v2
>
> chr14_GL000194v1
>
> chr14_GL000225v1
>
> chr14_KI270726v1
>
> chr15_KI270727v1
>
> chr16_KI270728v1
>
> chr17_GL000205v2
>
> chr1_KI270711v1
>
> chr1_KI270713v1
>
> chr22_KI270731v1
>
> chr22_KI270733v1
>
> chr22_KI270734v1
>
> chrUn_GL000195v1
>
> chrUn_GL000213v1
>
> chrUn_GL000216v2
>
> chrUn_GL000218v1
>
> chrUn_GL000219v1
>
> chrUn_GL000220v1
>
> chrUn_KI270442v1
>
> chrUn_KI270744v1
>
> chrUn_KI270750v1
>
> but a large number (131) still give warnings (attached).
>
>
> 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
> ------------------------------
> *From:* dev-bounces at ensembl.org <dev-bounces at ensembl.org> on behalf of
> Will McLaren <wm2 at ebi.ac.uk>
> *Sent:* 22 November 2016 10:01:25
> *To:* Ensembl developers list
> *Subject:* Re: [ensembl-dev] VEP 86 GRCh38 - alt contig names not
> recognized
>
> 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
>>
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
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>
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