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Table 3 Details of haplotypes from phasing a single-isolate VCF from hybrid Bd isolate SA-EC3 using GATK v4 HaplotypeCaller, HaplotypeTools (default settings), and WhatsHap (default settings)

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

  HaplotypeCaller HaplotypeTools WhatsHap
Number of haplotypes 5545 7975 9982
Total phased nucleotides 1,35,334 6,74,408 50,02,469
Haplotype Nmax (nt) 230 1083 8485
Haplotype N50 (nt) 26 115 1107
Haplotype N90 (nt) 13 44 314
Overlap with HT (default) (#haps) 2027 N/A 7948
Overlap with HT (nt) 44,157 N/A 6,58,713
Computational time N/A 41m56s 5m54s
  1. Rows include the number of haplotypes produced by each tool, the total number of nucleotides included in those haplotypes, the maximum haplotype length found (Haplotype Nmax), the Hap N50 and N90 (the shortest haplotype length that includes ≥ 50% and ≥ 90% of haplotype sequence, respectively.). The number of haplotypes (#haps) that overlap on the genome assembly with haplotypes produced by HaplotypeTools (HT), and the number of nucleotides (nt) in those haplotpes. Computational time is also given for HaplotypeTools and Whatshap, but omitted for GATK given its primary role was variant calling, which both HaplotypeTools and WhatsHap were also based on, and the time taken for phasing alone can neither be determined or distinguished from that process