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This wiki will contain all supplemental documentation for the PharmCAT repo.

General Structure

• VCF Requirements
• Preparing the VCF Files
• NamedAlleleMatcher 101
• Running PharmCAT
• Running the NamedAlleleMatcher
• Running the Reporter

Starting Points

• Genes to Call.

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
• CPIC Translation Data repo
• JSON-formatted CPIC guidelines (.zip file)
• Genes with Haplotype Definitions

How-To Guides

• Converting CPIC guideline grc38 positions to grc37

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