VEP chromosome name query

1

Hi,

I have been annotating my VCFs which has chromosome names such as chr1, chr2 etc. using a reference clinvar structural variation VCF which has chromosome names as 1, 2, etc. I am using the structural variation plugin of VEP.

Theoritically, VEP should throw an error due to wrong chromosome names, but it does not. Does VEP take care of the chromosome name by itself?


ensembl


VCF


annotation


VEP

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