Figure 2

PCF function to compute minor allele frequency. Here × and y are the inputs for one genotype read in from Alice and Bob's data, respectively. The low-order 16 bits of each input correspond to a control group, whereas the high-order 16 bits correspond to a case group. We begin by computing the aggregated count of the lexicographically lower (e.g. 'A' < 'G') nucleotide for each group across both parties. lowCt denotes this count for the aggregated control group, and likewise highCt for the control group. The lexicographically high counts are simply the total counts minus the low ones. We then decide which count is lower, and thus must represent the minor allele. Finally we perform a floating point adjustment, divide to obtain the frequency, and output the case and control MAFs to the terminal.