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Alignment Scores
The alignment scores of each read pair are based on a Bayesian model, where the probability of each mapping is inferred from the base qualities and the positions of the mismatches. The final mapping quality (MAPQ) is the alignment score, truncated to 60 for scores above 60, and corrected based on known ambiguities in the reference flagged during candidate mapping. Following alignment, reads are sorted. Further analysis is performed to identify duplicates and optionally to realign indels.
The alignment scores of each read pair are based on a Bayesian model, where the probability of each mapping is inferred from the base qualities and the positions of the mismatches. The final mapping quality is the alignment score, truncated to 60 for scores above 60. Following alignment, reads are sorted. Further analysis is performed to identify duplicates and optionally to realign indels.