Question: What are the GP, MP, and DC tags in the Cell Ranger DNA BAM file used for?
Answer: The definitions of these tags can be found at https://support.10xgenomics.com/single-cell-dna/software/pipelines/latest/output/bam. They can be used as a convenience to properly mark or identify duplicates. Use of these tags in any custom downstream analysis is discouraged as the tags will be deprecated (after version 1.0).
The tag values can be derived from other information in the BAM file. When an alignment starts at position x, and if the first n bases of the read are soft-clipped, then GP = x-n (assuming forward orientation). The same applies to the MP tag. Thus, for any read pair the GP and MP tags for one read will match the MP and GP tags, respectively, for the other read. We mark a read pair as a duplicate if it shares the same GP/MP tag values as another read pair.