The Somatic Mutation Comparison tool
You use the Somatic Mutation Comparison tool to
generate a filtered variant report for somatic variant detection. The tool is similar in both layout and function to the Variant Comparison tool. The tool filters variants based on comparison with a matched normal sample as well as a project with pooled normal samples to eliminate both non-somatic variants and artifacts that are the result of library preparation or alignment. You must load three different sequence alignment project (*.pjt) files that were aligned to the same reference sequence:
• The project file for a sequence alignment project for a cancerous tumor sample from a patient.
• The project file for the sequence alignment project for the matched normal sample, where the matched normal sample (for example, a blood sample) is from the same patient.
• The sequence alignment project file for the pool, where the pool consists of four to five normal samples that were aligned together in a single alignment project in the Project Wizard.
The tool then filters out the following variants based on your specified settings:
• All the variants that were found in the tumor sample project that were also found in the matched normal sample project.
• All the variants that were found in the tumor sample project that were also found in the pooled alignment project.