By Katrin Sangkuhl in PharmCAT — Apr 18, 2025

PharmCAT version 3.0.0 released

The PharmCAT version 3.0.0 release is now available and brings significant changes.

New highlights included:

Phase Set Support - Support for phase sets in VCF (PS genotype field).
New TSV Reports - Produce focused reports on allele calls that eliminate the complexity of PharmCAT's JSON reports.
Allele Frequency Analysis - Leverage the new TSV reports to run frequency analysis.
NAT2 Allele Calling - Enable calling NAT2 alleles with a new mechanism that uses frequency analysis to help call unphased data.
Required Positions - PharmCAT can now enforce minimum data requirements for calling some genes. For example, NAT2 requires data for 5 key variants.
- We are planning to use the "Required Positions" feature to provide warnings in the PharmCAT report if VCF files don't have coverage of AMP Tier 1 alleles. We'd like to hear from users if you agree with this and if so, where in the PharmCAT report you would expect to see this information (e.g. in the Gene Section).

For more details see the v3.0.0 release notes on GitHub.

The documentation on pharmcat.org is also significantly updated and restructured.

For feedback or to report issues, either email or submit a bug/feature request.