VEP synonyms file
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.
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Sowmya Pulapet •
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Please, be more specific on what you need... Do you want to create another file with just synonyms variants?
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.
a synonym file of what ?
A synonym file to match the chromosome names in my VCF file to the same in GFF file.
https://github.com/dpryan79/ChromosomeMappings
Thank you for your response. My annotation files are from Phytozome (https://phytozome-next.jgi.doe.gov/).