Using my own code, I would like to detect if tags are duplicated.
I wrote a script that tallies the number of tags which map to every position, with a different tally for the forward and reverse strands. For all positions that have multiple tags mapped to it, I keep one and discard the rest.
The count I get of duplicated reads is not the same as samtools rmdup.
Is there something extra that I am missing that samtools rmdup does?