[ensembl-dev] Ensembl VEP: local script assigned incorrect annotation to variants on chrY

[Sarah Hunt]

Hi Emma,

When did you pick up the cache files? There was a problem with the 
chromosome Y files initially produced for e!77 and they were updated on 
the ftp site on 11/11/2014. If you picked them up as soon as they were 
released, you may have the broken version.

We would recommend you switch to a newer version of the code. GRCh37 is 
still supported and recent versions of VEP are faster than the version 
you currently have.

Best wishes,

Sarah


On 01/04/2016 03:02, cy_jiang wrote:
> Hello there, I am using the VEP script (version 77) to analyse my 
> variation data locally. It works fine on almost all chromosomes except 
> chrY. For example, variant record "chrY 14107314" got annotation 
> "ENSG00000235649" when using the website VEP, which is correct. 
> However, when I use VEP locally, this record was assigned with 
> "ENSG00000165246". The genome reference I am using is GRCh37. My 
> command is shown below :perl 
> /home/software/ensembl-tools-release-77/scripts/variant_effect_predictor/variant_effect_predictor.pl 
> -i input.vcf -o output.vep.vcf –offline –dir_cache 
> /home/data/ensembl/cache –vcf –merged –force_overwrite –quiet –fork 10 
> –hgvs –assembly GRCh37 –everything Can anyone give me some clue on 
> this? Thank you very much! Best, Emma
>
>
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