[ensembl-dev] VEP warning

[Will McLaren]

Hi Alison,

It looks from the the path in your error message that your API is still
version 85.

If you are running the new (ensembl-vep) code, you should use the latest
(release/87) version of the ensembl, ensembl-variation and ensembl-funcgen
API checkouts. The INSTALL.pl script will download a set of these within
the ensembl-vep directory for you to use, or you may use git to update the
directories from the path in your error message.

Regards

Will McLaren
Ensembl Variation


On 15 February 2017 at 09:12, MEYNERT Alison <alison.meynert at igmm.ed.ac.uk>
wrote:

> I've been running the new VEP package on the v87 GRCh37 downloaded cache,
> and get a warning for just one of the lines in my input VCF.
>
>
> 20 34067454 . AT A
>
> WARNING: 63631 : Use of uninitialized value $cdna_position in pattern
> match (m//) at /exports/igmm/software/pkg/el7/libs/ensembl_api/85/
> ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 1901, <GEN4> line 57651.
>
> Use of uninitialized value $cdna_coord in concatenation (.) or string at
> /exports/igmm/software/pkg/el7/libs/ensembl_api/85/
> ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 1933, <GEN4> line 57651.
>
> Use of uninitialized value $exon_start_coord in addition (+) at
> /exports/igmm/software/pkg/el7/libs/ensembl_api/85/
> ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 703, <GEN4> line 57651.
>
> When I try inputting this variant to the GRCh37 web interface, it works.
> I also didn't get any warnings when running the old VEP package on the v86
> GRCh37 downloaded cache, and get the following hits:
>
>
> ENSG00000126001 ENST00000342580 intron_variant
>
> ENSG00000126001 ENST00000397527 intron_variant
>
> ENSG00000126001 ENST00000425096 downstream_gene_variant
>
> ENSG00000126001 ENST00000425934 downstream_gene_variant
>
> ENSG00000126001 ENST00000461386 downstream_gene_variant
> ENSG00000230155 ENST00000416260 intron_variant,non_coding_
> transcript_variant
>
> ENSG00000230155 ENST00000444933 intron_variant,non_coding_
> transcript_variant
>
> ENSG00000230155 ENST00000453914 intron_variant,non_coding_
> transcript_variant
>
>
> 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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