Difference between revisions of "Pharmacotyper"
Farmakorakel (talk | contribs) (Ny side: ==Pharmacotyper - getting relevant PGx variants from a patient VCF== The Pharmacotyper extracts relevant variants from a VCF returns ;allele matching : Match variants to PGx alleles by c…) |
Farmakorakel (talk | contribs) (→Pharmacotyper latest version) |
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| − | ==Pharmacotyper - | + | ==Pharmacotyper - PGx genotyping in terms of star alleles== |
| − | The Pharmacotyper | + | The Pharmacotyper is a collection of tools for genotyping of PGx alleles |
| − | ;allele matching | + | |
| + | ===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 [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. | ||
| + | |||
| + | ===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]] | : 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]] |
| + | |||
| + | We have coined the verb ''to pharmacotype'' for the action of the Pharmacotyper. | ||
Latest revision as of 13:13, 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.
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.
