In version 2.0, we have made substantial improvements and changes to the tool based in part on user feedback. Below we outline these features and provide links to read more about each one. We have also slightly reorganized and expanded the documentation found on the PharmCAT website to better support users.
We hope you will take a look and send any comments, questions or feedback to firstname.lastname@example.org.
Major PharmCAT v2.0 features:
- PharmCAT now includes available DPWG prescribing guidance (as annotated in the PharmGKB DB) in addition to CPIC recommendations. Read more about the genes and drugs included from DPWG and how they are sourced
- PharmCAT report has been redesigned for multiple recommendation sources
- Added functionality for research use only
- CYP2D6 diplotype calling based on SNPs and INDELs from a VCF file (does not include structural variants/CNVs). Warning: Because structural variation and haplotype can’t be determined from VCF, this functionality shouldn’t be used for clinical purposes.
- Partial and combination calls for novel combinations of PGx positions included in the PharmCAT allele definitions. This functionality helps users determine if a sample potentially contains a novel allele.
- Added support for the DPYD genotype based on the lowest activity score as described in CPIC’s fluoropyrimidine guideline (PMID: 29152729) for samples with more than two DPYD variants.
- Extended support of external genotype/phenotype input (see input and output examples and outside call format). This functionality allows users to include genetic test results from other sources in PharmCAT’s report.
- Reworked PharmCAT command line tool/arguments. These changes are not backwards compatible with previous PharmCAT versions.
- VCF Preprocessor updates
- Harmonized the VCF preprocessor command line arguments and flags with PharmCAT
- Unified the output file name patterns of the VCF preprocessor with what PharmCAT uses
- Added a few amenities, e.g., bcftools and bgzip version check, switch to .bgz file suffix for clarity