Pharmcat: Difference between revisions
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<code>$ pharmcat -vcf <sample_file> -o <output_dir></code> | <code>$ pharmcat -vcf <sample_file> -o <output_dir></code> | ||
Latest revision as of 20:19, 12 August 2022
Description
PharmCAT: Pharmacogenomics Clinical Annotation Tool. 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.
System Variables
- HPC_PHARMCAT_DIR - installation directory
Additional Information
$ 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.