HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes

BMC Bioinformatics

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)

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 N_max), 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

ISSN: 1471-2105