Applications of GenomeVIP. (A) Principal component analysis of germline SNV and indel predictions for nonrelated 1000 Genomes Project Phase 1 samples from three populations: (red) CHB; (green) FIN; (blue) YRI. (B) True-positive (TP) and false-positive (FP) rates for somatic SNV calls novel to dbSNP. Performance of VarScan and Strelka callers individually (red, blue) and in combination (green, purple) are evaluated before and after exploratory false-positives filtering using multiple parameter combinations, in which VSR is the minimum number of variant-supporting reads. (C) GenomeVIP performance on ICGC Pan-Cancer Pilot-50 somatic mutation calling for one matched sample pair, in which the colors correspond to the number of pipelines predicting the same variant. (D) Performance statistics. (E) De novo recall performance (blue), as compared to published experimental validation results, and filtered call set size (red) for SNV calling in NA12878 as a function of PVSR, the number of variant-supporting reads in parental genomes NA12891 and NA12892. (F) dbSNP concordances of germline SNVs and indels, as called by GenomeVIP (darker shading) and GotCloud (lighter shading), for the samples described in A.