VEP synonyms file

Question

[Sowmya Pulapet]

Hello everyone, I am using VEP for variant annotation. If you could help me with creating a synonym file to match chromosome name in vcf and annotation sources to use for custom annotation, it would be great.

Thanks in advance.

[brunobsouzaa]

Please, be more specific on what you need... Do you want to create another file with just synonyms variants?

[Sowmya Pulapet]

Apologies! I want to match the chromosome names in my VCF file to the same in GFF file. For that I would like to create a chr_synonym file.

[Pierre Lindenbaum]

a synonym file of what ?

[Sowmya Pulapet]

A synonym file to match the chromosome names in my VCF file to the same in GFF file.

[Pierre Lindenbaum]

https://github.com/dpryan79/ChromosomeMappings

[Sowmya Pulapet]

Thank you for your response. My annotation files are from Phytozome (https://phytozome-next.jgi.doe.gov/).