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TASSEL 5

VCAP Scan

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TASSEL 5

Home
Home
Download
Download
- Nightly Builds
Getting Started
Getting Started
- Installation
  Installation
- User Manual
  User Manual
  - Introduction
  - File Menu
    
    File Menu
    
    Open / Open As
    
    Data FAQ
    
    Save As / Export
  - Data Menu
    
    Data Menu
    
    Synonymizer
    
    Joins
    
    Merge Genotype Tables
    
    Separate
    
    Homozygous Genotype
    
    Set Low Depth Genos To Missing
    
    Transform Phenotype
    
    Numerical Genotype
    
    ABH Genotype
    
    Thin Sites By Position
    
    Create Hybrid Genotypes
    
    Geno Summary
  - Impute Menu
    
    Impute Menu
    
    FSFHap Imputation
    
    Numerical Impute
    
    Missing Phenotype Imputation
  - Filter Menu
    
    Filter Menu
    
    Filter Genotype Table Sites
    
    Filter Genotype Table Taxa
    
    Filter Traits
  - Analysis Menu
    
    Analysis Menu
    
    Linkage Disequilibrium
    
    Distance Matrix
    
    Kinship
    
    Cladogram
    
    Pedigree Relationship Matrix (A)
    
    Combined A and G Matrix (H)
    
    MDS
    
    PCA
    
    Remove NaN from Distance Matrix
    
    GLM
    
    MLM
    
    Weighted MLM
    
    Genomic Selection
    
    Stepwise
    
    Fast Association
    
    VCAP Scan
    
    Association Analysis using GLM
    
    Association Analysis using MLM
    
    Estimation of Kinship using Genetic Markers
    
    Principal Component Analysis
  - Results Menu
    
    Results Menu
    
    Archaeopteryx Tree
    
    LD Plot
    
    Chart
    
    QQ Plot
    
    Manhattan Plot
  - GBS Menu
  - Help Menu
  - Frequently Asked Questions
  - Executing TASSEL
  - User Guide (PDF)
  - Appendix
    Appendix
    
    Nucleotide Codes
    
    Depth Encodings
    
    Tutorial Datasets
    
    References
- Pipelines
  Pipelines
  - Pipeline Tutorial
  - Pipeline Reference
  - GBSv2 Pipeline
  - Archived
    Archived
    
    UNEAK Pipeline
    
    Pan-genome Atlas (PanA)
    
    Cassava Production Pipeline
    
    Pipeline CLI (v3 / v4)
Community
Community
- Get Involved
  Get Involved
  - Contributing
  - Code of Conduct
- Developer
  Developer
Version History

Variance Component Annotation Pipeline (VCAP) Scan Plugin¶

Tassel Variance Component Annotation Pipeline (VCAP) Documentation
Tassel VCAP Tutorial

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