The article describing the Pharmacogenomics Clinical Annotation Tool (PharmCAT) and a pilot validation using GeT-RM samples was recently published in Clinical Pharmacology & Therapeutics.
PharmCAT (1) extracts variants specified in guidelines from a genetic dataset derived from sequencing or genotyping technologies; (2) infers haplotypes and diplotypes; and (3) generates a report containing genotype/diplotype-based annotations and guideline recommendations.
In this initial version, the tool only considers variants contained in the allele definition files, which are based on CPIC guidelines and provides CPIC recommendations in the output. PharmCAT assumes the sample VCF file has already undergone extensive quality control. Requirements for the VCF files are accessible in GitHub.
PharmCAT was highly concordant with the GeT-RM data and discordant results are discussed in detail in the article and supplemental material [add link to journal or to PharmCAT.org, if we post it there].
Seeking community input and testing. With this initial beta release of PharmCAT, the pharmacogenomics community is asked to support the continuing evaluation of this freely available tool by running VCF samples, documenting issues and successfully identifying variants. GitHub can be used to communicate feedback.
PharmCAT is available under the Mozilla Public License (MPL 2.0) for the scientific and clinical community to review, test, and improve.