toc.json

[
  {"Introduction": "introduction.md"},
  {"Get Started": [
    {"Overview": "GetStarted/overview.md"},
    {"Set Up X11 Forwarding": "GetStarted/set-up-x11-forwarding.md"},
    {"Download and Open Genvisis": "GetStarted/download-and-open-genvisis.md"},
    {"Find Required Raw Data Files": "GetStarted/find-required-raw-data-files.md"},
    {"Create Pedigree and Linker Files": "GetStarted/set-up-pedigree-and-linker.md"},
    {"Set Up Directories": "GetStarted/set-up-directories.md"},
    {"Create a New Project": "GetStarted/create-a-new-project.md"},
    {"Import an Existing Project": "GetStarted/import-an-existing-project-into-genvisis.md"},
    {"Resources Directory": "GetStarted/resources-directory.md"}
  ]},
  {"Run the Genvisis Workflow": [
    {"Introduction to the Workflow": "RunTheGenvisisWorkflow/introduction-to-the-workflow.md"},
    {"Illumina Data Sets": [     
      {"Create Marker Positions": "RunTheGenvisisWorkflow/create-marker-positions-illumina.md"},
      {"Parse Sample Files": "RunTheGenvisisWorkflow/parse-sample-files-illumina.md"},
      {"Run Marker BLAST Annotation": "RunTheGenvisisWorkflow/run-marker-blast-annotation-illumina.md"},
      {"Transpose Data into Marker-Dominant Files": "RunTheGenvisisWorkflow/transpose-data-illumina.md"}
    ]},
    {"Affymetrix Data Sets": [
      {"Create Marker Positions": "RunTheGenvisisWorkflow/create-marker-positions-affymetrix.md"},
      {"Process Affymetrix CEL Files": "RunTheGenvisisWorkflow/process-affymetrix-cel-files.md"},
      {"Transpose Marker Files to Sample Files": "RunTheGenvisisWorkflow/transpose-marker-files-affymetrix.md"},
      {"Run Marker BLAST Annotation": "RunTheGenvisisWorkflow/run-marker-blast-annotation-affymetrix.md"}
    ]},
    {"All Data Sets": [
      {"Compute GCMODEL File": "RunTheGenvisisWorkflow/compute-gcmodel-file.md"},
      {"Compute SampleQC Metrics": "RunTheGenvisisWorkflow/compute-sample-qc-metrics.md"},
      {"Identify Excluded Samples": "RunTheGenvisisWorkflow/identify-excluded-samples.md"},
      {"Run Sex Checks": "RunTheGenvisisWorkflow/run-sex-checks.md"},
      {"Generate AB Lookup File": "RunTheGenvisisWorkflow/generate-ab-lookup-file.md"},
      {"Create PLINK Genotype Files": "RunTheGenvisisWorkflow/create-plink-genotype-files.md"},
      {"Run GWAS QC": "RunTheGenvisisWorkflow/run-gwas-qc.md"},
      {"Run Ancestry Checks": "RunTheGenvisisWorkflow/run-ancestry-checks.md"},
      {"Annotate Sample Data File": "RunTheGenvisisWorkflow/annotate-sample-data-file.md"},
      {"Compute Population BAF Files": "RunTheGenvisisWorkflow/compute-population-baf-files.md"},
      {"Create Sex-Specific Centroids and Filter PFB File": "RunTheGenvisisWorkflow/create-sex-specific-centroids.md"},
      {"Call CNVs": "RunTheGenvisisWorkflow/call-cnvs.md"},
      {"Filter CNVs": "RunTheGenvisisWorkflow/filter-cnvs.md"},
      {"Process CNVs and Create HMM File": "RunTheGenvisisWorkflow/process-cnvs-and-create-hmm-file.md"},
      {"Call CNVs Using Optimized HMM File": "RunTheGenvisisWorkflow/call-cnvs-using-optimized-hmm-file.md"},
      {"Filter Optimized CNVs": "RunTheGenvisisWorkflow/filter-optimized-cnvs.md"},
      {"Identify Samples To Use In CNV Analysis": "RunTheGenvisisWorkflow/identify-samples-to-use-in-cnv-analysis.md"},
      {"Run CNV Analysis Pipeline": "RunTheGenvisisWorkflow/run-cnv-analysis-pipeline.md"},
      {"Generate Genotype Mask": "RunTheGenvisisWorkflow/generate-genotype-mask.md"},
      {"Run Marker QC Metrics": "RunTheGenvisisWorkflow/run-marker-qc-metrics.md"},
      {"Run Further Analysis QC": "RunTheGenvisisWorkflow/run-further-analysis-qc.md"},
      {"Identify Mosaic Chromosomal Arms": "RunTheGenvisisWorkflow/identify-mosaic-chromosomal-arms.md"},
      {"Identify Problematic Markers": "RunTheGenvisisWorkflow/identify-problematic-markers.md"},
      {"Generate Principal Components": "RunTheGenvisisWorkflow/generate-principal-components.md"},
      {"Create PC-Corrected Project": "RunTheGenvisisWorkflow/create-pc-corrected-project.md"},
      {"Create Mitochondrial Copy-Number Estimates File": "RunTheGenvisisWorkflow/create-mitochondrial-copy-number-estimates-file.md"},
      {"Create VCF Files for Imputation": "RunTheGenvisisWorkflow/create-vcf-files-for-imputation.md"}
    ]}
  ]},
  {"Run a PC-Corrected Project": [
    {"Overview": "RunAPCCorrectedProject/overview.md"},
    {"Workflow": "RunAPCCorrectedProject/workflow.md"}
  ]},
  {"Workflow Output": [
    {"Illumina Data Sets": "WorkflowOutput/output-illumina.md"},
    {"Affymetrix Data Sets": "WorkflowOutput/output-affymetrix.md"},
    {"All Data Sets": "WorkflowOutput/output-all.md"}
  ]},
  {"Visualize Workflow Results": [
    {"Scatter Plot": "VisualizeWorkflowResults/scatter-plot.md"},
    {"Trailer Plot": "VisualizeWorkflowResults/trailer-plot.md"},
    {"Comp Plot": "VisualizeWorkflowResults/comp-plot.md"},
    {"Mosaic Plot": "VisualizeWorkflowResults/mosaic-plot.md"},
    {"Ancestry Plot": "VisualizeWorkflowResults/ancestry-plot.md"},
    {"Sex Plot": "VisualizeWorkflowResults/sex-plot.md"},
    {"Custom Plot": "VisualizeWorkflowResults/custom-plot.md"},
    {"QQ Plot": "VisualizeWorkflowResults/qq-plot.md"},
    {"Forest Plot": "VisualizeWorkflowResults/forest-plot.md"},
    {"Manhattan Plot": "VisualizeWorkflowResults/manhattan-plot.md"}
  ]},
  {"Interpret Results":[
    {"CNV Analysis Results": "InterpretResults/cnv-analysis-results.md"}
  ]},
  {"Scripting": [
    {"Running Genvisis via Script": "Scripting/running-genvisis-via-script.md"}
  ]},
  {"Command Line": [
    {"Help Within Genvisis": "CommandLine/help-within-genvisis.md"},
    {"Commands in Genvisis": "CommandLine/commands-in-genvisis.md"}
  ]},
  {"Menu": "menu.md"},
  {"Toolbar": "toolbar.md"},
  {"Appendix A - Genome Studio": [
    {"GenomeStudio Background": "AppendixAGenomeStudio/genomestudio-background.md"},
    {"Install GenomeStudio": "AppendixAGenomeStudio/install-genomestudio.md"},
    {"Create a New Project": "AppendixAGenomeStudio/create-a-new-project.md"},
    {"Open an Existing Project": "AppendixAGenomeStudio/open-an-existing-project.md"},
    {"Add Samples to an Existing Project": "AppendixAGenomeStudio/add-samples-to-an-existing-project.md"},
    {"Recluster Samples Before Exporting to Genvisis": "AppendixAGenomeStudio/recluster-samples-before-exporting.md"},
    {"Export Reports for Further Analysis in Genvisis": "AppendixAGenomeStudio/export-reports-for-further-analysis.md"},
    {"Exclude Samples": "AppendixAGenomeStudio/exclude-samples.md"},
    {"Export Reports with a Subset of SNPs": "AppendixAGenomeStudio/export-reports-with-a-subset-of-snps.md"},
    {"Sex Determination Explained": "AppendixAGenomeStudio/sex-determination-explained.md"},
    {"Finding Illumina Manifest Files": "AppendixAGenomeStudio/finding-illumina-manifest-files.md"}
  ]},
  {"Appendix B - Amazon S3": [
    {"Overview": "AppendixBS3/overview.md"},
    {"Set Up Credentials for S3 Access": "AppendixBS3/set-up-credentials.md"},
    {"Create a Bucket and Grant Users Access": "AppendixBS3/create-a-bucket.md"},
    {"Upload Files with S3": "AppendixBS3/upload-files-with-s3.md"},
    {"Link Genvisis to an S3 Environment": "AppendixBS3/link-genvisis-to-s3-environment.md"}
  ]},
  {"Appendix C - TOPMed Imputation Server": [
    {"TOPMed Imputation Server": "AppendixCTOPMedImputation/topmed-imputation-server.md"}
  ]}
]