VEP chromosome name query

Question

[prasundutta87]

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?

[Ram]

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.

[prasundutta87]

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

[Ram]

It looks like the plugin is designed to check both with and without the chr prefix: https://github.com/Ensembl/VEP_plugins/commit/7c4c055bdb60bc02af460763cb83d48c62246947

If the output looks fine (you should manually test a few entries), you can rest assured that the prefix doesn't really matter.

[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!

Answer 1

[Emily]

VEP is very clever, you're fine.

[prasundutta87]

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