Example 1 - All Reference

This is a collection of example files that demonstrate input and output files from a single run of PharmCAT. For more information about running PharmCAT, read the documentation.

Input

First, a properly formatted single-sample VCF file with all positions specified.

• example input VCF

This is an example of an optional file of outside diplotype calls. This one specifies a CYP2D6 call.

• example outside calls

Output

Named Allele Matcher output

The Named Allele Matcher component generates both HTML and JSON files with detailed information about how data in the sample VCF matches up with haplotype definitions.

• example matcher HTML
• example matcher JSON

Phenotyper output

The Phenotyper component takes data from the Named Allele Matcher and combines it with outside call data to assign function and metabolizer values.

• example phenotype JSON

Reporter output

The 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.

• example report HTML
• example report JSON

Example 2 - Some Non-Reference Alleles

This is a collection of example files with CYP2C19 *2/*2 and CYP2B6 *1/*6 diplotypes. One input VCF file that contains the source variant data and the corresponding output files that would result from running that input file.

Input VCF

• example2 input VCF

Output

• example2 matcher HTML
• example2 matcher JSON
• example2 phenotype JSON
• example2 report HTML
• example2 report JSON