[ensembl-dev] VEP warning

[MEYNERT Alison]

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
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