Question: There are variants between phase blocks in Long Ranger. Why were they not joined?
Answer: Since Long Ranger is a reference based tool it reports homozygous and heterozygous SNVs. Only the heterozygous SNVs are informative for phasing. In order to phase a molecule, there must be more than one read from that molecule that overlaps a heterozygous SNV. You can explore this by going to the HAPLOTYPES view in the Loupe Browser and navigate to your region of interest. It may look something like this:
Is this example, there are two phase blocks outlined in black. The blue circles, green triangles, and orange squares represent SNVs and small indels. It looks like there are enough variants to connect the blocks and even extend them. However, when you use the homozygous button to hide the homozygous SNVs and display only the heterozygous SNVs, you will see this:
The region between the phase blocks is void of SNVs that are informative for phasing as are the regions following the blocks. Thus Long Ranger is not able to join or extend the phase blocks.