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.
UGP Variant Calling
- UGP Variant Calling Protocol
- UGPp - a lightweight NGS analysis pipeline implementing the UGP variant calling protocol.
- The HCI Informatics team have created a pipeline using Tomato2 that implements the UGP Variant Protocol
The UGP and the UCGD are developing a variant protocol that utilizes the FreeBayes variant caller from the Marth Lab. We are in the process of optimizing this protocol and benchmarking its performance on various datasets.