This is a collection of example files that demonstrate input and output files from a single run of PharmCAT. For more inforamtion about running PharmCAT, read the documentation.
First, a properly formatted single-sample VCF file with all positions specified.
This is an example of an optional file of outside diplotype calls. This one specifies a CYP2D6 call.
NamedAlleleMatcher component generates both HTML and JSON files with detailed information about how data in the
sample VCF matches up with haplotype definitions.
Phenotyper component takes data from the
NamedAlleleMatcher and combines it with outside call data to assign
function and metabolizer values.
Reporter component takes data from the
Phenotyper and matches phenotypes to information found in CPIC guideline
data. This data is visible in an HTML report and also in a JSON file for machine parsing.