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Somatic Quality Scores
After the prescoring steps, Mantra uses a probabilistic model to estimate Q-scores. Specifically, given counts of anomalous and normal reads in tumor and normal BAM files, Mantra estimates the probability of observing a given or more extreme number of anomalous reads in a tumor sample using the Fisher Exact Test. This estimate is written as a Phred-scaled score; for example, Q-score = -10 log10(Prob variant is somatic). Inspection of somatic variant calls in both real and simulated data suggests that Q-score threshold of 30 should provide a good trade-off between sensitivity and specificity. The maximum achievable score is 60; the lowest is 0.