[ensembl-dev] VEP v76

Will McLaren wm2 at ebi.ac.uk
Mon Sep 29 12:06:08 BST 2014


Hi Konrad,

I can't replicate the issue I'm afraid. A couple of things to try:

1) Update your ensembl-variation checkout from GitHub - there may have been
a bug fix that caught this already

2) Download again and re-index your FASTA file

3) If neither of the above works, run perl with -d to jump into the Perl
debugger, then:
- press c, enter (you might need to do this twice to skip past a breakpoint)
- the script should then fail and give you a backtrace of where it failed
in the code hierarchy, this would help me debug.

perl -d ./ensembl-tools-release-76/scripts/variant_effect_predictor/
variant_effect_predictor.pl --everything --vcf --allele_number --no_stats
--cache --offline --dir ./vep/ --force_overwrite --fasta
./vep/homo_sapiens/76_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
--tabix -i ./test/test.vcf.gz -o test.vep.vcf.gz --gencode_basic

Regards

Will McLaren
Ensembl Variation

On 28 September 2014 20:04, Konrad Karczewski <konradk at broadinstitute.org>
wrote:

>  Hi dev team,
>
> When running v76 of VEP (with GRCh37), I'm getting a bunch of these errors
> (command below):
>
>  substr outside of string at
> /humgen/atgu1/fs03/konradk/ensembl-tools-release-76/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/Sequence.pm
> line 511.
> Use of uninitialized value $ref_allele in string eq at
> /humgen/atgu1/fs03/konradk/ensembl-tools-release-76/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/Sequence.pm
> line 514.
> Use of uninitialized value in concatenation (.) or string at
> /humgen/atgu1/fs03/konradk/ensembl-tools-release-76/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/Sequence.pm
> line 643.
>
>  perl ./ensembl-tools-release-76/scripts/variant_effect_predictor/
> variant_effect_predictor.pl --everything --vcf --allele_number --no_stats
> --cache --offline --dir ./vep/ --force_overwrite --fasta
> ./vep/homo_sapiens/76_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
> --tabix -i ./test/test.vcf.gz -o test.vep.vcf.gz --gencode_basic
>
> Here's one line it fails on, for instance:
>
> 1       69995   .       G       C       282.63
> VQSRTrancheSNP99.60to99.80      AC=1
>
> Thanks!
>
> -Konrad
>
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