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Impact of preprocessing (trimming, PCR duplicate removal). F1 Scores for mixtures M1–M4 for the three polymerases, with fastp’s default trimming + quality filtering (fastp), Picard-Tools MarkDuplicates (markdup), and without preprocessing (none) by using mutserve variant caller, with the default parameters in all three experiments (1% threshold, per base quality Phred score 20, BAQ turned off).
