UserManualfor.PDFVIP

User Manual for Intelligent Prediction and Association Tool (Version 1.1) Last updated on Apr 24, 2017 Table of Contents 1. Getting start 2. Interface 2-1 Import files 2-2 Create a project 2-3 File formats 2-4 Covariates and kinship 2-5 Define input arguments 2-6 Run an analysis 2-7 Check the results 2-8 Files remove 3. GWAS and GS 3-1 GAPIT 3-2 FarmCPU 3.3 PLINK 3.4 rrBLUP 4. Support 5. Citation 1. Getting start Before launching iPat, remember to place folder libs to the path where iPat.jar exists. iPat can function normally only when it is in the same folder as ‘libs’. The operation environment need to meet the following requirement: Operation System: Mac OS X. Java Runtime Environment (JRE) : Version 8 or later. R: Version 3.4.0 or later. After set up all the thing mentioned previously, iPat is now ready to go. Double-click on iPat.jar to launch iPat. 2. Interface 2.1 Import files At beginning, iPat will show nothing but an icon iPat at the top of screen. Users can import files simply by dragging and dropping. 2.2 Create a project After importing the files, double clicking on anywhere in iPat to create a new project. Build linkages between this project and all the files planed to be analyzed. A linkage can be built by dragging one object over one another. 2.3 File formats iPat can recognize and work fine with different formats, which include hapmap, numeric, vcf and plink. Imported file set need to have identical names and correct extension name if they need to be converted to a proper format. For example, if you want to perform GWAS using VCF format in FarmCPU, files set should be named as: data.vcf and data.txt. The table below shows examples of files and its extension name for the corresponded format: