Difference between revisions of "Pharmacotyper"
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===Pharmacotyper latest version=== | ===Pharmacotyper latest version=== | ||
| − | The current version of Pharmacotyper is based on published tools in a Singularity container, and pending introduction in our [[Bioinformatic pipeline]]. | + | 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 | ; HLA typing | ||
Revision as of 13:11, 27 February 2019
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.
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.
