Re-call SNVs after phasing

[pontushojer]

I was browsing through the 10x genomics longranger algorithms section and found the do a second variant calling after phasing, see the quote below.

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.

Possibly this could be a good addition.

Issue copied from FrickTobias/BLR#211