• User Manuel for iPat
  • Why iPat?
  • 1 Get started
    • 1.1 Windows users
    • 1.2 Mac OS users
  • 2 Interface and Usage
    • 2.1 Workflow
      • Create a new module
      • Import files
      • Choose an analysis
      • Config and run
      • Monitor progress
      • Inspect results
    • 2.2 Global settings
      • 2.2.1 Working directory
      • 2.2.2 Phenotype
      • 2.2.3 Quality Control
    • 2.3 GWAS
      • 2.3.1 GAPIT
      • 2.3.2 FarmCPU
      • 2.3.3 PLINK
    • 2.4 GS
      • 2.4.1 gBLUP and rrBLUP
      • 2.4.2 BGLR
    • 2.5 GWAS-assisted GS
    • 2.6 Format converter
    • 2.7 Multi-thread is supported
  • 3 Formats
    • 3.1 Input formats
      • 3.1.1 Genotype
      • 3.1.2 Phenotype
      • 3.1.3 Map
      • 3.1.4 Covariates
      • 3.1.5 Kinship
    • 3.2 Output formats
      • 3.2.1 Figures
      • 3.2.2 Tabular results
  • 4 Step by Step Tutorial
    • 4.1 GWAS in GAPIT
      • Prepare PLINK files
      • Import files
      • Define GAPIT
      • Inspect results
    • 4.2 K-fold cross-validation GS in BGLR
      • Prepare VCF files
      • Import files
      • Define BGLR
      • Inspect results
    • 4.3 GWAS-assisted GS in rrBLUP
      • Import files
      • Define FarmCPU (GWAS)
      • Define rrBLUP (GS)
      • Inspect Progress
    • 4.4 Convert Hapmap to PLINK format
      • Prepare Hapmap files
      • Import files
      • Define BGLR
      • Inspect results
  • References
  • Article on Bioinformatics

iPat: Intelligent Prediction and Association Tool

4.4 Convert Hapmap to PLINK format

This section will demonstrate that how to convert Hapmap files into PLINK-formatted files.

Prepare Hapmap files

Fig. Check if the format is Hapmap

Import files

Fig. Import Hapmap files into iPat

Define BGLR

Fig. Define the conversion

Inspect results

Fig. Inspect results