Nextflow Modules
Showing module(s) with keyword "pharmcat"
| Module | Keywords | Description |
|---|---|---|
| nf-core/pharmcat/matcher | vcf pharmcat matcher PGx | The Named Allele Matcher is responsible for calling diplotypes from variant call data. While it is designed to be used in the PharmCAT pipeline, it can also be run independently. The Named Allele Matcher does not currently support structural variants, including gene copy number. If structural variants are detected in the VCF data, it will be ignored and a warning will be issued. If it detects more than the expected number of alleles in the GT column of the VCF, only the first two alleles will be used and a warning will be issued. On haploid chromosomes, only the first allele will be used. |
| nf-core/pharmcat/phenotyper | vcf pharmcat phenotyper PGx | The PharmCAT Phenotyper is a core module of the Pharmacogenomics Clinical Annotation Tool that translates patient diplotypes into specific, actionable metabolizer phenotypes (e.g., Poor Metabolizer). It operates by analyzing the JSON output from the Named Allele Matcher, mapping these results to established clinical guidelines (such as CPIC) to predict drug response. |
| nf-core/pharmcat/reporter | pharmcat report PGx | The Reporter module is responsible for generating a report with genotype-specific expert-reviewed drug prescribing recommendations for clinical decision support. |