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Menu

  • File
    • New Project
    • Import Project
    • Select Project
    • Delete Project
    • Properties Editor
    • Open Project Directory
    • Preferences
    • Check for updates
    • Exit
  • Data
    • Audit Linker and Pedigree files
    • Audit Samples and Markers (generate paragraph)
    • Map .csv files to IDs
    • Add data to SampleData
    • Project Workflow
  • Quality
    • Scan for CNPs
    • Filter marker metrics
    • Tally marker annotations
    • Tally without determining dropped markers (much faster)
    • Tally all reclustered markers
  • Plots
    • Scatter
    • Trailer
    • Comp
    • Mosaic
    • Ancestry
    • Sex
    • Custom
    • QQ
    • Forest
    • Manhattan
  • Tools
    • Export to PLINK format
      • Generates PLINK files using the FID/IID IDs in linker.txt
      • Exports only high quality samples and no duplicates
      • In contrast, the Create PLINK Files step generates files using a DNA/DNA scheme that the Run GWAS QC step requires, and includes all samples.
      • Inputs
        • Pedigree File
        • Target Markers FIle
          • A list of markers to base the PLINK files on.
          • One marker per row.
          • Markers in the project, but not in the target file, will be ignored.
          • Leave this option blank to use all markers in PLINK file generation.
        • Cluster Filter File
          • The list of cluster filter files is generated from any file ending with “*clusterFilters.ser” in the project’s data/ directory. The clusters can be manually added from within the ScatterPlot module.
        • AB Lookup File
        • Export Filetype
          • Export files as text or binary
        • PLINK Output Fileroot
          • Files will be generated with this name.
          • Eg. plink will generate plink.bim, plink.bed, plink.fam.
          • Eg. plink/subset/plink will generate a sub directory named subset/ containing plink.bim, plink.bed, plink.fam.
          • There is an Overwrite option that will replace pre-existing files with the same name.
        • GC Cutoff
          • The minimum GC quality score for a sample to be exported.
          • Default is 0.15.
    • Export to VCF format [DEPRECATED]
    • Export for imputation [DEPRECATED]
    • Generate PennCNV files
    • Compute MedianLRR for Regions
    • Parse raw PennCNV results files
    • Parse BPM to CSV file
    • Compute custom centroids file
    • De Novo CNV
    • Export CNVs to Pedfile format
    • Parse workbench files
    • Principal Components
      • Generate manhattan plots
      • Generate PC crosstabs
      • Generate data column matrix
    • Rebuild marker details files
  • Help
    • Contents
    • Search
    • About