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
Chapter 3
Formats