[ensembl-dev] Resolved issue with release 91 VEP cache files

William McLaren wm2 at ebi.ac.uk
Tue Dec 19 15:19:41 GMT 2017


Dear VEP users,

An issue was found with the following VEP cache files made available for release 91 on 11th December 2017 at ftp://ftp.ensembl.org/pub/release-91/variation/VEP/:

homo_sapiens_merged_vep_91_GRCh37.tar.gz
homo_sapiens_merged_vep_91_GRCh38.tar.gz
homo_sapiens_refseq_vep_91_GRCh37.tar.gz
homo_sapiens_refseq_vep_91_GRCh38.tar.gz
homo_sapiens_vep_91_GRCh37.tar.gz
homo_sapiens_vep_91_GRCh38.tar.gz

This issue would manifest as either:
 - missing or incorrect allele frequency data from 1000 Genomes, ESP or gnomAD (using —af_1kg, —af_esp, —af_gnomad or —everything)
 - repeated warnings/errors like the following:

Argument "" isn't numeric in subroutine entry at /homes/user/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource.pm line 258, <$__ANONIO__> line 134935.
Argument "A/G" isn't numeric in subroutine entry at /homes/user/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource.pm line 258, <$__ANONIO__> line 134935.

These cache files have now been replaced with corrected versions. If you downloaded any of the above files between 11th and 18th December inclusive, please replace them by re-running the INSTALL.pl script.

Regards

Will McLaren
Ensembl Variation
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