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Running PharmCAT

• Running PharmCAT
• Running the NamedAlleleMatcher
• Running the Reporter

PharmCAT requires Java 1.8 or newer.

Documentation

• VCF Requirements
• Preparing the VCF Files
• NamedAlleleMatcher 101
• NamedAlleleMatcher 201

Contributing

• Tooling
• Java Coding Conventions
• How to Git
• Building PharmCAT

Join us in the PharmCAT Slack.

Important Links & Data

• CPIC Site
• CPIC Guideline Publications
• List of annotated CPIC guidelines
• Genes with Haplotype Definitions

How-To Guides

• Converting CPIC guideline grc38 positions to grc37

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