Changes

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 [https://github.com/humanlongevity/HLA xHLA]** ; ADME typing: For other genes we use [https://github.com/inumanag/aldy 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.

The first version of the Pharmacotype was based on custom methodsfor 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]]