[ensembl-dev] VEP error - mouse cache

[cj5 at sanger.ac.uk]

Hi,

We are having problems running the VEP script version 2.4 in offline mode using the mouse cache, eg:

cat mouse.vcf | variant_effect_predictor.pl --species mus_musculus --gene --hgnc --format vcf -o mouse.vep.txt --force_overwrite --cache
--dir /lustre/scratch105/projects/g1k/ref/vep_cache --offline

Can't call method "length" on unblessed reference at
/software/vertres/lib/all/ensembl/66/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1758, <STDIN> line 11.

The example vcf looks looks this:

##fileformat=VCFv4.1
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##INFO=DP,1,Integer,"Total Depth"
##INFO=AC,-1,Integer,"Allele count in genotypes"
##INFO=AN,1,Integer,"Total number of alleles in called genotypes"
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  AJ
1       3000054 .       AGGGGGGGGGG     AGGGGGGGGGGG    36.5    PASS    AC=2;AN=34      GT:PL:DP:SP:GQ  1/1:74,39,0:13:0:99

It looks like a problem with the cache itself, because if we simply change the position 3000054  to 13000054 (for example), it works. We
tried downloading and re-installing the cache files but the problem persists. Could you please advise?

Thanks
Chris