Fig. 2

Comparisons of haplotypes for the hybrid Bd isolate SA-EC3, generated by GATK v4 HaplotypeCaller physical phasing, HaplotypeTools and WhatsHap. A The length in nucleotides of haplotype pairs vs the difference between those haplotypes pairs (%). The red line indicates the minimum haplotype length used for all analysis, and the red arrow indicates the haplotype pairs illustrated in part B of this figure. B HaplotypeTools’ utility script HaplotypePlacer constructs haplotype trees with FastTree. Among the longest representative haplotype pairs (shown by the red arrow) are shown including supercontig 1.7 positions 1,335,923–1,336,143 for HaplotypeCaller, supercontig 1.17 positions 206,141–207,223 for HaplotypeTools and supercontig 1.4 positions 319,655–328,139 for WhatsHap. In each of these examples, one haplotype is closest to BdCAPE. For HaplotypeTools and WhatsHap that have several advantages over HaplotypeCaller’s physical phasing presented, the second haplotype is closest to BdGPL