What is a Protocol?

A protocol is a template for analysis which includes predefined filters, the list of required and associated samples and a corresponding report template. 

When starting a new analysis in TGex, you will be asked to select a protocol for analyzing your sample(s). By default, your account should contain a few default protocols, categorized into a few groups, which include:

Rare Genetics

• Germline - Single Sample - This case is commonly used to analyze germline samples when you only have access to the affected sample.
• Germline - Trio - This case is commonly used to analyze a rare genetics case when you have access to samples for the parents and the affected.
• Mitochondria - This protocol is commonly used to analyze data from Mitochondrial DNA.
• Germline - SV - This protocol is used to analyze structural variations available in VCF format or TSV.

Tumor

• Tumor Biopsy - Single Sample - This case is commonly used to analyze somatic samples when you have no access to the germline sample.
• Tumor Biopsy - with Germline - This case is commonly used to analyze somatic samples together with their germline counterparts.

TGex also includes default protocols for cancer and carrier screening, which are available for premium (paid) accounts. Premium accounts can customize their protocols based on the needs of the lab.