After phasing, the variant caller is invoked separately in 'haploid mode' on reads from each phased haplotype. This step boosts the sensitivty of the variant calls by calling low-allele fraction variants that are the dominant allele on one haplotype. Variants called in this phase will be tagged with HAPLOCALLED=1 in the INFO field.
I was browsing through the 10x genomics longranger algorithms section and found the do a second variant calling after phasing, see the quote below.
Possibly this could be a good addition.