Figure 2.

An illustration of two iterations of ExHap. This figure illustrates the first two iterations and the final result of ExHap on a simplified example. Each iteration consists of 2 parts: derivation of the consensus string and filtering of chromosomes for congruence. In Iteration 1, Part 1, we compute the most frequent sequence or string of 9 SNPs from our haplotype matrix. Then we add the first 3 SNPs from this string to the emerging consensus string. In Part 2, we filter the chromosomes based on whether or not each matches the consensus string using a matching rule. In this example, the matching rule is that at least 2 of 3 contiguous SNPs must match. SNPs that do not match are highlighted in gray. In Iteration 2, Part 1, the position of the derivation window is adjusted by 3 SNPs. In Part 2, we compare SNPs 2-6 of each chromosome to SNPs 2-6 of the consensus by inspecting 3 SNPs at a time. Thus, we must inspect SNPs 2-4, 3-5, and 4-6. The processes described here are repeated over the entire haplotype matrix. The final result shows the congruent chromosomes and the percentage of allele identity for each chromosome. The size of the derivation window and the number of SNPs to record are user-configurable. In this example, the size of the derivation window is 9 and the number of SNPs to record is 3. The size of the filter window, the number of SNPs that must match in this window, and the window offset are also user-configurable. In this example, the size of the filter window is 3, the number of matching SNPs is 2, and the offset is 1