Question: Why don't my reads have HP tags in the BAM file?
Answer: Not all reads can be confidently assigned to a haplotype (HP). Reads that lack barcodes (BX) or molecule assignments (MI) are not assigned to haplotypes. A read may have a BX tag and a MI tag but still not have enough evidence to confidently phase. Reads with no heterozygous variants (hets) or only a few hets with low confidence phasing may not have a HP tag. Reads with contradictory phasing information will also not be assigned a haplotype.
For more information please see Barcoded BAM.