Identify unique SNPs specific to pre-defined clades or clusters across large data-set

Question

[goatsrunfaster]

I'm looking to identify SNPs unique to specific pre-defined clades or clusters across a large bacterial WGS data-set. I am able to do this manually by loading my .vcf file with my .fasta reference into Gingr (with my tree), but scrolling across 5 million reads is giving me a headache. Anyone know of any executable or script out there that might help with this? Thanks in advance!