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VCF Issue while running PharmCAT pipeline

Status: Open.

#223 In PharmGKB/PharmCAT;

· Sillar-codes opened on Feb 8, 2026

Preprocessing Failure: KeyError and Coordinate Corruption (Pos 1) during VCF Normalization

Status: Open.

#222 In PharmGKB/PharmCAT;

· lbombini opened on Feb 3, 2026

phase information is removed when preprocessing multiallelic sites

Status: Open.

#221 In PharmGKB/PharmCAT;

· hudja opened on Feb 3, 2026

Pharmcat not interpreting phased vcf?

Status: Open.

#219 In PharmGKB/PharmCAT;

· Dafna-Mozand opened on Jan 14, 2026

Support BCF

enhancement

Status: Open.

#212 In PharmGKB/PharmCAT;

· markwoon opened on Sep 2, 2025

UGT1A1 *80+*28 and *80+*37 output

Status: Open.

#197 In PharmGKB/PharmCAT;

· katrinsangkuhl opened on Oct 22, 2024

Document genes that shouldn't be set to reference

Status: Open.

#193 In PharmGKB/PharmCAT;

· markwoon opened on Aug 21, 2024

Publish to cloud tooling providers like Dockstore, AnVIL, etc

feature

Status: Open.

#188 In PharmGKB/PharmCAT;

· whaleyr opened on Jul 22, 2024

FHIR / HL7 support

feature

help wanted

Status: Open.

#186 In PharmGKB/PharmCAT;

· markwoon opened on Jul 10, 2024

Duplicated CYP2D6 diplotypes in matcher JSONs

Status: Open.

#184 In PharmGKB/PharmCAT;

· BinglanLi opened on Jun 11, 2024

Capture homozygous reference INDELs based on individual positions

Status: Open.

#182 In PharmGKB/PharmCAT;

· BinglanLi opened on Apr 24, 2024

PharmCAT Telemetry

feature

Status: Open.

#179 In PharmGKB/PharmCAT;

· markwoon opened on Mar 27, 2024