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Fig. 2 | BMC Genomics

Fig. 2

From: HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data

Fig. 2

ROC curves of DNMs called by FreeBayes, TrioDeNovo, GATK, and DeNovoGear by optimal parameter setting, and the improved ROC curves after applying HAPDeNovo (red line). Sequencing depth threshold is varied from 10 (start of each plot line, leftmost point) to 30 (end of each plot line, rightmost point). FP (False Positive): Number of false positive DNMs. Sensitivity: Number of true positive DNMs divided by the total number of true positive plus false negative DNMs. GL: Genotype Likelihood; DQ: De Novo Quality; PL: Posterior Likelihood; PP: Posterior Probability. Blue curves show the sensitivity and number of FPs at default settings (no GL and no PL thresholds for FreeBayes and GATK, respectively). Green curves show the sensitivity and number of FP at optimal parameter settings (GL = −50 for FreeBayes, DQ = 7 for TrioDeNovo, PL = 450 for GATK, and PP = 3E-5 for DeNovoGear). Red curves show the performance after applying HAPDeNovo

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