Issues

• Data refresh will fail on the objCls short names the ClinPGx PharmCAT export is switching to

  PharmGKB/PharmCAT#243 · Filter by author markwoon opened on Sep 28, 2026
  

• CYP2D6 outside calls with non-identical gene copies (+, e.g. *68+*4, *36+*10) resolve to Indeterminate / no recommendation

  Bug

  PharmGKB/PharmCAT#242 · Filter by author townes-spec opened on Sep 25, 2026
  3

  

• Running PharmCAT new version on previosly called gVCFs

  PharmGKB/PharmCAT#241 · Filter by author AliKhanbazi opened on Sep 19, 2026

• VCF preprocessor converts an explicit missing genotype (./.) to 0/0 during catalog ALT completion

  PharmGKB/PharmCAT#240 · Filter by author Luker121 opened on Sep 16, 2026

• DPYD phenotype assigment

  question
  PharmGKB/PharmCAT#234 · Filter by author ursikajanzic opened on May 22, 2026
  1

  

• DPYD phenotype output discrepancy and genotype normalization behavior in PharmCAT 3.0.1

  question
  PharmGKB/PharmCAT#233 · Filter by author ranijames opened on May 11, 2026
  6

  

• Request: PharmCat Artifact Without Logback Dependency

  help wanted
  PharmGKB/PharmCAT#228 · Filter by author gorupria opened on Apr 9, 2026
  4

• Coordinate Corruption in Symbolic Alleles

  preprocessor
  PharmGKB/PharmCAT#225 · Filter by author markwoon opened on Feb 17, 2026
  1

• phase information is removed when preprocessing multiallelic sites

  need more infopreprocessor
  PharmGKB/PharmCAT#221 · Filter by author hudja opened on Feb 3, 2026
  1

• Support BCF

  enhancement
  PharmGKB/PharmCAT#212 · Filter by author markwoon opened on Sep 2, 2025

• UGT1A1 *80+*28 and *80+*37 output

  PharmGKB/PharmCAT#197 · Filter by author katrinsangkuhl opened on Oct 22, 2024

• Document genes that shouldn't be set to reference

  PharmGKB/PharmCAT#193 · Filter by author markwoon opened on Aug 21, 2024
  2

• Publish to cloud tooling providers like Dockstore, AnVIL, etc

  feature
  PharmGKB/PharmCAT#188 · Filter by author whaleyr opened on Jul 22, 2024
  9

  

• FHIR / HL7 support

  featurehelp wanted
  PharmGKB/PharmCAT#186 · Filter by author markwoon opened on Jul 10, 2024
  3

• Duplicated CYP2D6 diplotypes in matcher JSONs

  PharmGKB/PharmCAT#184 · Filter by author BinglanLi opened on Jun 11, 2024

• Capture homozygous reference INDELs based on individual positions

  PharmGKB/PharmCAT#182 · Filter by author BinglanLi opened on Apr 24, 2024
  2

• PharmCAT Telemetry

  feature
  PharmGKB/PharmCAT#179 · Filter by author markwoon opened on Mar 27, 2024
  

• Support for various array data in tabular (CSV/TSV/XLSX) format

  featurehelp wanted
  Feature

  PharmGKB/PharmCAT#177 · Filter by author whaleyr opened on Mar 25, 2024
  2

• OA and CNV Data from QuantStudio 12K Flex

  PharmGKB/PharmCAT#172 · Filter by author Estefany2081 opened on Feb 9, 2024
  13

• Add warning to summary table

  PharmGKB/PharmCAT#163 · Filter by author katrinsangkuhl opened on Nov 15, 2023
  

• Adding Genes to Pharmcat Report

  featurehelp wanted
  PharmGKB/PharmCAT#145 · Filter by author pbrennan-mvz opened on Jun 29, 2023
  12

• Update Galaxy on PharmCAT release

  PharmGKB/PharmCAT#143 · Filter by author markwoon opened on Jun 8, 2023
  

• Add PharmCAT Docker image to GCR/Artifact Repository

  PharmGKB/PharmCAT#140 · Filter by author markwoon opened on May 18, 2023
  

• PDF Support

  PharmGKB/PharmCAT#132 · Filter by author markwoon opened on Mar 16, 2023
  2

• Update warfarin workflow to include CYP4F2

  PharmGKB/PharmCAT#112 · Filter by author markwoon opened on Sep 29, 2022
  4