VarScan2

Description

VarScan2 is a somatic variant calling pipeline used in GDC whole exome sequencing (WXS) and targeted sequencing harmonization.

Overview

VarScan2 is one of the four pipelines used for WXS and targeted sequencing somatic variant calling at the GDC. Somatic variant calling is performed with VarScan2 using tumor and normal alignments and generates single-nucleotide polymorphism (SNP) data.

Input

• Tumor BAM - WXS or Targeted Sequencing
• Normal BAM - WXS or Targeted Sequencing

Output

• VCF (Data Type: Raw Simple Somatic Mutation)

References

1. DNA Seq Processing at the GDC
2. Somatic Variant Calling Workflow

External Links

• VarScan
• VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.
• Overview of GDC Harmonization Workflows
• GDC Data Portal

Categories: Workflow Type