What tools are there that enable (more sophisticated) analysis of phased VCF files?

Question

[vlaufer]

Hello,

I have phased several dozen whole genomes I am analyzing in order to see if certain tagSNPs seem to lie on the same chromosomes as putative causal variants.

In doing this, I have been using mostly awk, shell, and python scripts and writing the programs myself.

However, I am also wondering what tools might already exist that people are using to carry-out more sophisticated analysis of phased NGS data, whether whole exome or whole genome data.

Thanks!