pharmcat

Description

pharmcat website

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:

Commentary: TE Klein, MD Ritchie. PharmCAT: A Pharmacogenomics Clinical Annotation Tool. Clinical Pharmacology & Therapeutics (2018) 104(1):19-22. Methods paper: K Sangkuhl & M Whirl-Carrillo, et al. Pharmacogenomics Clinical Annotation Tool (PharmCAT). Clinical Pharmacology & Therapeutics (2020) 107(1):203-210.

Categories

biology, phylogenetics