VEP synonyms file

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2.5 years ago

Sowmya Pulapet ▴ 70

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.

Ensembl-VEP annotation synonyms • 1.4k views

ADD COMMENT • link 2.5 years ago by Sowmya Pulapet ▴ 70

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

ADD REPLY • link 2.5 years ago by brunobsouzaa ▴ 840

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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.

ADD REPLY • link 2.5 years ago by Sowmya Pulapet ▴ 70

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a synonym file of what ?

ADD REPLY • link 2.5 years ago by Pierre Lindenbaum 164k

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

ADD REPLY • link 2.5 years ago by Sowmya Pulapet ▴ 70

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https://github.com/dpryan79/ChromosomeMappings

ADD REPLY • link 2.5 years ago by Pierre Lindenbaum 164k

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

ADD REPLY • link 2.5 years ago by Sowmya Pulapet ▴ 70

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