Question: How does Cell Ranger DNA detect PCR or optical duplicates? Do you use picard or samtools?
Answer: We look for groups of read pairs where the (corrected) 10x-barcode, contig ID, 5' position (including soft-clipping), mate contig ID, and mate 5' position are all shared. All but one of these pairs is assumed to be a duplicate. The pipeline determines these with custom code, instead of farming out to e.g. picard or samtools.
For more information about these algorithms please see Cell Ranger DNA Algorithms Overview.