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

[MEYNERT Alison]

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<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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