What it does

This tool is supposed to remove alignments to the same position in the genome from the Bismark mapping output (both single and paired-end SAM files), which can arise by e.g. excessive PCR amplification. If sequences align to the same genomic position but on different strands they will be scored individually.

Note that deduplication is not recommended for RRBS-type experiments!

For single-end alignments only use the start-coordinate of a read will be used for deduplication.

For paired-end alignments the start-coordinate of the first read and the end coordinate of the second read will be used for deduplication.