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

[cy_jiang]

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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