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

[MEYNERT Alison]

Thank you Will, that's good to know.


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: 05 December 2016 15:50:40
To: Ensembl developers list
Subject: Re: [ensembl-dev] VEP 86 GRCh38 - alt contig names not recognized

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<mailto: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<mailto: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<mailto:dev-bounces at ensembl.org> <dev-bounces at ensembl.org<mailto:dev-bounces at ensembl.org>> on behalf of Will McLaren <wm2 at ebi.ac.uk<mailto: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<mailto: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<mailto: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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