Figure 1

Receiver operating characteristic for SNV optimization. An ROC for the filtering parameters used in SNV detection optimization. Red points indicate the calculated specificity for certain fixed sensitivity levels. The blue line indicates the calculated specificity and sensitivity in 0.5% increments along the entire range of parameters. The optimal set of parameters for the GATK is given in Table 2. SNVs were then divided into either a ‘called or ‘not called’ category based on these metrics and the current set of filters being used. The following metrics were obtained from the Unified Genotyper: read depth, strand bias, haplotype score, homopolymer run length, total positional mapping quality, number of null mapping qualities, total positional quality, total quality by depth, and genotype quality (DP, FS, HaplotypeScore, HRun, MQ, MQ0, QUAL, QD, GQ). These SNVs were then hard filtered using the Variant Filtration Walker according to the given set of parameters, as in Table 2.