pharmcat¶

Description¶

A tool to extract all CPIC guideline gene variants from a genetic dataset (represented as a VCF file), interpret the variant alleles, and generate a report.

Environment Modules¶

Run module spider pharmcat to find out what environment modules are available for this application.

Environment Variables¶

HPC_PHARMCAT_DIR - installation directory

Additional Usage Information¶

Here is an example use case for Pharmcat:

$ pharmcat -vcf <sample_file> -o <output_dir>

Citation¶

If you publish research that uses pharmcat you have to cite it as follows:

Klein, T. E., & Ritchie, M. D. (2018). PharmCAT: A Pharmacogenomics Clinical Annotation Tool. Clinical Pharmacology & Therapeutics, 104(1), 19-22. https://doi.org/10.1002/cpt.928

Sangkuhl, K., Whirl-Carrillo, M., Woon, M., Klein, T. E., Altman, R. B., & Ritchie, M. D. (2020). Pharmacogenomics Clinical Annotation Tool (PharmCAT). Clinical Pharmacology & Therapeutics, 107(1), 203-210. https://doi.org/10.1002/cpt.1568

Categories¶

biology, phylogenetics