Difference between revisions of "Pharmcat"
Jump to navigation
Jump to search
(Created page with "Category:SoftwareCategory:BioinformaticsCategory:BiologyCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|pharmcat}} |{{#vardefine:url|...") |
|||
| (One intermediate revision by one other user not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software | + | [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|pharmcat}} | |{{#vardefine:app|pharmcat}} | ||
| Line 30: | Line 30: | ||
|}} | |}} | ||
<!--Run--> | <!--Run--> | ||
| − | {{#if: {{#var: exe}}|==Additional Information== | + | {{#if: {{#var: exe}}1|==Additional Information== |
<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.