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  "Title": "Defining Local Haplotype Variants for Use in Trait Association\nand Trait Prediction Analyses",
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  "Authors@R": "c(person(\"Tessa\", \"MacNish\", email = \"tessa.macnish@research.uwa.edu.au\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0009-0008-8985-7348\")), person(\"Hawlader\", \"Al-Mamun\", role = \"ctb\"), person(\"Thomas\", \"Bergmann\", role = \"ctb\"), person(\"Mitchell\", \"Bestry\", role = \"ctb\"), person(\"Jacob\", \"Marsh\", role = \"ctb\"), person(\"David\", \"Edwards\", role = \"ctb\"))",
  "Description": "A local haplotyping tool for use in trait association and\ntrait prediction analyses pipelines. HaploVar enables users\ntake single nucleotide polymorphisms (SNPs) (in VCF format) and\na linkage disequilibrium (LD) matrix, calculate local\nhaplotypes and format the output to be compatible with a wide\nrange of trait association and trait prediction tools. The\nlocal haplotypes are calculated from the LD matrix using a\nclustering algorithm called density-based spatial clustering of\napplications with noise (DBSCAN) (Ester et al., 1996) <ISBN:\n1577350049>.",
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  "Date/Publication": "2026-10-09 05:08:30 UTC",
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      "title": "Brassica napus genotype data in VCF format",
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        "data.frame"
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      "rows": 490,
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      "tojson": true
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      "title": "Collate define_haplotypes Lists",
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    {
      "page": "define_haplotypes",
      "title": "Define Haplotypes",
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        "define_haplotypes"
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      "title": "Define Haplotypes Globally",
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    {
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      "title": "Identify Haplotype Variants",
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        "haplotype_variants"
      ]
    },
    {
      "page": "haplotype_variants_global",
      "title": "Identify Haplotype Variants Globally",
      "topics": [
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    {
      "page": "LD",
      "title": "Linkage Disequilibrium Matrix",
      "topics": [
        "LD"
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    },
    {
      "page": "vcf",
      "title": "Brassica napus genotype data in VCF format",
      "topics": [
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        "Preparing inputs",
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        "Collate Define Haplotypes",
        "Define Haplotypes Globally",
        "Identify Haplotypes Variants",
        "Collate Haplotypes Variants",
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