Fig. 3

Conceptual idea of the DeDup method. Paired-end forward and reverse reads resulting from two fragments are drawn in red and merged reads are drawn in blue. Although the two merged reads stem from two different DNA fragments, SAMtools rmdup removes the read with the lower overall sum of base qualities, as only the starting position of the mapped reads is taken into account. DeDup takes both mapping positions (start and end) into account, and in this case would keep both reads