Pharmacotyper - PGx genotyping in terms of star alleles

The Pharmacotyper is a collection 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 Singularity container, and pending introduction in our Bioinformatic pipeline.

HLA typing
For HLA typing we use xHLA
ADME typing
For other genes we use Aldy

Note that 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, 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.