Genotyping data (Pyrosequencing)

I performed the genotyping of breast cancer patients. I am willing to analyse the data for haplotypes analysis, cluster view and phylogenetic tree. In pyrosequencing the results comes in the form of pyrogram (attachment page 1), but I am still confused to find out the minor allele frequency (MAF) in samples and what allele (major or minor) I should used to calculate this (attachment page 2).

Secondly, I will be grateful if someone guide me any other test/analysis that I could performed by using this data.

Thanks