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→Pharmacotyper latest version
==Pharmacotyper - getting relevant PGx variants from genotyping in terms of star alleles==The Pharmacotyper is a patient VCFcollection of tools for genotyping of PGx alleles ===Pharmacotyper latest version===The current version of Pharmacotyper is based on published tools (working on BAM files) in a Python script Singularity container, and pending introduction in our [[Bioinformatic pipeline]]. ; HLA typing: For HLA typing we use [https://github.com/humanlongevity/HLA xHLA]; ADME typing: For other genes we use [https://github.com/inumanag/aldy Aldy] Note that extracts relevant variants from neither Aldy nor xHLA are free software, and it remains to figure out the permissions to use the methods in a clinical setting. ===Pharmacotyper legacy version===The first version of the Pharmacotype was based on custom methods for finding PGx alleles in a VCF and returns, inspired by PharmCAT.;allele matching
: Match variants to PGx alleles by custom method. Return list of possible PGx alleles in the nomenclature of the OWL ontology of [[Pharmacoracle]]
;haplotype queries
: Return variants in terms of queries to [[Pharmacoracle]]
We have coined the verb ''to pharmacotype'' for the action of the Pharmacotyper.