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CaVEMan

Description

CaVEMan (Cancer Variants through Expectation Maximization) is a somatic variant calling algorithm used in the GDC for whole genome sequencing (WGS) data harmonization. It detects single nucleotide variants (SNVs) in tumor samples by comparing them to matched normal samples.

Overview

CaVEMan is one of the four pipelines used for WGS variant calling at the GDC. Variant calling is performed with CaVEMan using tumor and normal alignments and generates single nucleotide variation (SNV) data.

Input

  • Tumor BAM - WGS
  • Normal BAM - WGS

Output

  • VCF (Data Type: Raw Simple Somatic Mutation)

References

  1. DNA-Seq Analysis Pipeline
  2. Whole Genome Sequencing Variant Calling

Categories: Workflow Type