Foreignness for mouse data

[saraahwallace]

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]

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]

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