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VEP chromosome name query

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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written by prasundutta87 prasundutta87

Are you using VEP command line? If yes, what is your command?

Side note: It's ensEMBL, not ensemble. There's no e at the end.

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written by Ram Ram

Oh! my bad..thanks for correcting me..

My command is:

vep -i input.vcf -o output.vcf --offline --dir_cache VEP_genomes --vcf --force_overwrite --plugin StructuralVariantOverlap,file=nstd102.GRCh38.variant_call.vcf.gz
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written by prasundutta87 prasundutta87

Thanks a lot for sharing this! Although, I did rename the chromosomes just to be sure. But its good to know this. Thanks a lot again!

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written by prasundutta87 prasundutta87

1 answer

VEP is very clever, you're fine.

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written by Emily Emily

Haha! I am sure of that, Emily! :-)

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written by prasundutta87 prasundutta87

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