Difference between revisions of "Pharmacotyper"
Farmakorakel (talk | contribs) (→Pharmacotyper - getting relevant PGx variants from a patient VCF) |
Farmakorakel (talk | contribs) (→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] | |
| + | ** [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 | |
| − | + | ** 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. | 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.
- HLA typing
Pharmacotyper legacy version
The first version of the Pharmacotype was based on custom methods, 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.
