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andrewrech / antigen.garnish

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Foreignness for mouse data #155

Closed saraahwallace closed 1 month ago

saraahwallace commented 11 months ago

Hi,

Just wanted to check before I got too in depth into the download for this, does the foreignness calculation have compatibility with mice?

leeprichman commented 11 months ago

Hi Saraah,

Yes, foriegnness calculation can be performed for mouse, and it is automatically detected based on the HLA type input (if "H-2" is detected the species is set to mouse. That said, foreignness for mice is adapted from the method in PMID: 29132144 using mouse data deposited in the IEDB. Their study was only using human data however, so mouse foreignness calculation is untested for its biological relevance.

saharlccSCSU commented 9 months ago

Hi, We are trying to run antigen garnish on a GATK generated vcf. We get the error below when calling garnish_variants(file). Any insights?

All variants processed Error in stri_replace_all_regex(string, pattern, fix_replacement(replacement), : Illegal argument. (U_ILLEGAL_ARGUMENT_ERROR) Calls: garnish_variants ... -> -> stri_replace_all_regex Execution halted