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andrewrech / antigen.garnish

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Backwards compatibility with hg19 #139

Closed ARChakravarthy closed 3 years ago

ARChakravarthy commented 3 years ago

I notice the metadata files you have in the extdata folder are to do with GRCh38 ; is the package compatible with hg19 variant calls, or is the use of liftOver recommended? It would be helpful if the documentation clarified this.

andrewrech commented 3 years ago

Thank you @ARChakravarthy for your interest in the software. I clarified in the README that GRCh38 is required.

Yes, you will need to use liftOver. A specific GRCh38 transcript version number is required to make sure the peptides are registered correctly.