Fig. 1

Modifications to the LRP and HLI algorithms to deal with library haplotypes with missing data. a In this example, we generated haplotypes using two different SNP arrays, as indicated by green and blue haplotypes. If the shared markers between two haplotypes are identical (shown in red), then the two haplotypes can be merged into one haplotype. To ensure the two haplotypes are the same haplotype, we set a minimum number of alleles that must be shared. Note that, in reality, both blue and green markers will be distributed along the length of the haplotype. b In this example, we generated haplotypes using three different SNP arrays. Finding the new purple haplotype allowed us to recognise that the green, purple, and blue haplotypes are actually the same haplotype