Utah Genome Project

The Utah Genome Project has developed a detailed variant calling protocol based on the GATK HapoltypeCaller. This protocol very closely follows the GATK Best Practices for variant calling on DNAseq data, however here we provide detailed and versioned protocol that includes exact command lines for each step in the analysis as well as links to accessory datasets.

Variant Analysis Pipeline

• UGP Variant Calling Protocol
• cApTUrE - a lightweight NGS analysis pipeline implimenting the UGP variant calling protocol)
• The HCI Informatics team have created a pipeline using Tomato2 that impliments the UGP Variant Protocol