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  "Title": "Data management of large-scale whole-genome sequence variant\ncalls using GDS files",
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  "Date": "2026-05-23",
  "Authors@R": "c(person(\"Xiuwen\", \"Zheng\", role=c(\"aut\", \"cre\"),\nemail=\"zhengx@u.washington.edu\", comment=c(ORCID=\"0000-0002-1390-0708\")),\nperson(\"Stephanie\", \"Gogarten\", role=\"aut\", email=\"sdmorris@uw.edu\"),\nperson(\"David\", \"Levine\", role=\"ctb\"),\nperson(\"Cathy\", \"Laurie\", role=\"ctb\"))",
  "Description": "Data management of large-scale whole-genome sequencing\nvariant calls with thousands of individuals: genotypic data\n(e.g., SNVs, indels and structural variation calls) and\nannotations in SeqArray GDS files are stored in an\narray-oriented and compressed manner, with efficient data\naccess using the R programming language.",
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  "Date/Publication": "2026-05-23 06:40:12 UTC",
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        "SeqArray"
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        "seqGDS2BED"
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      "page": "seqCheck",
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    {
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        "seqClose,SeqVarGDSClass-method"
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    },
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    {
      "page": "seqEmptyFile",
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      "title": "Example files",
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    {
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      "topics": [
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    {
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    {
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      "topics": [
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    {
      "page": "seqOpen",
      "title": "Open a SeqArray GDS File",
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      "topics": [
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    {
      "page": "seqParallel",
      "title": "Apply Functions in Parallel",
      "topics": [
        "seqParallel",
        "seqParApply"
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    {
      "page": "seqParallelSetup",
      "title": "Setup/Get a Parallel Environment",
      "topics": [
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        "seqMulticoreSetup",
        "seqParallelSetup"
      ]
    },
    {
      "page": "seqRecompress",
      "title": "Recompress the GDS file",
      "topics": [
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      ]
    },
    {
      "page": "seqResetVariantID",
      "title": "Reset Variant ID in SeqArray GDS Files",
      "topics": [
        "seqResetVariantID"
      ]
    },
    {
      "page": "seqSetFilter",
      "title": "Set a Filter to Sample or Variant",
      "topics": [
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        "seqFilterPush",
        "seqResetFilter",
        "seqSetFilter",
        "seqSetFilter,SeqVarGDSClass,ANY-method",
        "seqSetFilter,SeqVarGDSClass,GRanges-method",
        "seqSetFilter,SeqVarGDSClass,GRangesList-method",
        "seqSetFilter,SeqVarGDSClass,IRanges-method",
        "seqSetFilterAnnotID",
        "seqSetFilterChrom",
        "seqSetFilterPos"
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    },
    {
      "page": "seqSetFilterCond",
      "title": "Set a Filter to Variant with Allele Count/Freq",
      "topics": [
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    {
      "page": "seqSNP2GDS",
      "title": "Convert SNPRelate Format to SeqArray Format",
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    },
    {
      "page": "seqStorageOption",
      "title": "Storage and Compression Options",
      "topics": [
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    },
    {
      "page": "seqSummary",
      "title": "Summarize a SeqArray GDS File",
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      ]
    },
    {
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      "title": "Get the parameters in the GDS system",
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      "title": "Transpose Data Array",
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      "title": "Apply Function Over Variant Units",
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    },
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        "seqUnitSubset"
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    {
      "page": "seqUnitFilterCond",
      "title": "Filter unit variants",
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      "title": "SeqVarGDSClass",
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        "rowRanges,SeqVarGDSClass-method",
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        "SeqVarGDSClass-class"
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    },
    {
      "page": "seqVCF_Header",
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      "topics": [
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    },
    {
      "page": "seqVCF_SampID",
      "title": "Get the Sample IDs",
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    },
    {
      "page": "seqVCF2GDS",
      "title": "Reformat VCF Files",
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