Fig. 2: Comparison of GDC somatic variant caller pipelines.
From: Uniform genomic data analysis in the NCI Genomic Data Commons
The Venn Diagram on the left (a) shows the overlap among four GDC somatic callers. Among all clean variants, 56.0% have been identified by all four callers, 15.1% by three callers, 14.0% by two callers, and 14.9% by only one caller. The Venn Diagram on the right (b) shows recall rate of validated TCGA variants by GDC somatic callers. Among 115,476 TCGA validated variants collected, 3.2% are not recalled by any of the GDC pipelines; 1.2% are recalled by only one pipeline; 9.4% are recalled by two pipelines; 14.6% are recalled by three pipelines; and 71.6% are recalled by all four GDC pipelines.
