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GATK4 MuTect2 Tumor-Only

Description

GATK4 MuTect2 Tumor-Only is a somatic variant calling pipeline utilized in the GDC for analyzing tumor-only whole exome sequencing (WXS) and targeted sequencing data without normal samples.

Overview

GATK4 MuTect2 Tumor-Only is a pipeline used for WXS and targeted sequencing somatic variant calling at the GDC. Somatic variant calling is performed with GATK4 MuTect2 Tumor-Only using tumor alignments and generates single nucleotide variants (SNVs) data.

Input

  • Tumor BAM - WXS or Targeted Sequencing

Output

  • VCF (Data Type: Raw Simple Somatic Mutation)

References

  1. DNA-Seq Analysis Pipeline
  2. Tumor-Only Variant Calling Workflow

Categories: Workflow Type