[ensembl-dev] VEP v76

[Konrad Karczewski]

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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