Mutect2 Specifications

Process Details

• Name: mutect2
• Process UUID: sx0vks86s2ssxezfr82lpbon95tejk
• Process Group: gatk4

Overview

Mutect2 is a somatic variant caller that identifies single nucleotide variants (SNVs) and small insertions/deletions (indels) in tumor samples by comparing them against matched normal controls. This process is specifically designed for cancer genomics applications where distinguishing somatic mutations from germline variants is critical for downstream analysis.

This process is implemented in Bash, which invokes GATK's Mutect2 tool for somatic variant calling.

Key Functionality

• Somatic Variant Detection: Identifies mutations present in tumor samples but absent in matched normal controls
• Multi-sample Processing: Handles multiple control and treatment BAM files simultaneously
• Statistical Modeling: Uses sophisticated statistical models to distinguish true somatic variants from sequencing artifacts
• Quality Filtering: Applies built-in quality filters to reduce false positive variant calls

Input/Output Specification

Inputs

Required Inputs

• Input Directory

  • Description: Directory containing organized BAM files with controls and treatments subdirectories
  • Format: Directory structure with controls/ and treatments/ subdirectories containing BAM files

• Genome Dictionary

  • Description: Reference genome dictionary file required for GATK operations
  • Format: .dict file

Outputs

• VCF File
  • Description: Compressed VCF file containing identified somatic variants with associated quality metrics and annotations
  • Format: .vcf.gz file

Parameters & Settings

This process uses default GATK Mutect2 parameters and does not expose additional configurable parameters in the Foundry UI.

References & Resources

• Tool Documentation: GATK Mutect2 Documentation
• Related Papers: Benjamin, D., Sato, T., Cibulskis, K., Getz, G., Stewart, C., & Lichtenstein, L. (2019). Calling somatic SNVs and indels with Mutect2. bioRxiv. doi: 10.1101/861054