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Table 4 HaplotypeTools’ utility script HaplotypePlacer constructs haplotype trees with FastTree and identifies the closest relative to each

From: HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes

Lineage BdAsia1 BdAsia2 BdCAPE BdCH BdGPL
HaplotypeCaller (nt) 2556 1637 5180 2418 7089
HaplotypeCaller (%) 14 9 27 13 38
HaplotypeTools (nt) 52,806 55,341 3,22,642 51,476 3,14,161
HaplotypeTools (%) 7 7 41 6 39
Whatshap (nt) 3,86,839 2,58,519 43,96,845 2,61,089 44,56,306
Whatshap (%) 4 3 45 3 46
Overlapping phase groups 889 940 1344 758 1018
Overlapping phased positions (OPP) 1941 2131 3457 1661 2487
OPP Same phase (nt) 1758 1922 3421 1486 2467
OPP Same phase (%) 91 90 99 89 99
OPP Cross-over (nt) 183 209 36 175 20
OPP Cross-over (%) 9 10 1 11 1
  1. Hybrid Bd isolate SA-EC3 haplotypes from GATK v4 HaplotypeCaller physical phasing, HaplotypeTools and WhatsHap were analysed using HaplotypePlacer, finding that the majority of haplotypes from each of the three tools are closest in those trees to BdGPL (38–46%) and BdCAPE (27–45%). A HaplotypeTools utility script was used to compare phasing between SA-EC3 and each of the lineages. For each comparison, the script identified overlapping phase groups, comprising overlapping phased positions (OPP), which were either in the same phase, or showed evidence of crossovers