Difference between revisions of "Pharmacotyper"

(Pharmacotyper - getting relevant PGx variants from a patient VCF)
(Pharmacotyper - PGx genotyping in terms of star alleles)
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===Pharmacotyper latest version===
 
===Pharmacotyper latest version===
 
The current version of Pharmacotyper is based on published tools in a Singularity container.
 
The current version of Pharmacotyper is based on published tools in a Singularity container.
;HLA typing
+
 
: [https://github.com/humanlongevity/HLA xHLA]
+
# HLA typing
: [https://github.com/inumanag/aldy Aldy]
+
** [https://github.com/humanlongevity/HLA xHLA]
 +
** [https://github.com/inumanag/aldy Aldy]
  
 
===Pharmacotyper legacy version===
 
===Pharmacotyper legacy version===
 
The first version of the Pharmacotype was based on custom methods, inspired by PharmCAT.
 
The first version of the Pharmacotype was based on custom methods, inspired by PharmCAT.
;allele matching
+
# 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]]
+
** 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
+
# haplotype queries
: Return variants in terms of queries to [[Pharmacoracle]]
+
** Return variants in terms of queries to [[Pharmacoracle]]
  
 
We have coined the verb ''to pharmacotype'' for the action of the Pharmacotyper.
 
We have coined the verb ''to pharmacotype'' for the action of the Pharmacotyper.

Revision as of 10:22, 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 in a Singularity container.

  1. HLA typing

Pharmacotyper legacy version

The first version of the Pharmacotype was based on custom methods, inspired by PharmCAT.

  1. 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
  1. haplotype queries

We have coined the verb to pharmacotype for the action of the Pharmacotyper.