I am completely new to sequence analysis and a want to perform a GWAS analysis using an Illumina HumanOmni5 BeadChip. I received data of my 16 samples, which incluce jpeg and idat files 3 tables in txt format (full data, snp and sample).
I was looking for a recommended Workflow (any suggestions would be of great help to me) and Tools to analyse my data. I understand that I have to perform quality control of the Chip data before I can start the actual GWAS analysis. GWASTools seemed a proper tool for quality control and PLINK for subsequent analysis. I have some problems finding out about the details...
1. Which tools should I use (being new to the field)? Is there a tool (freeware) that can perform all necessary steps? What is the difference between the tasks GenomeStudio can perform and additional tools like GWASTools oder PLINK? Is PLINK also able to do all necessary qc steps?
2. Which of the data files for my Illumina-Chip do I have to read into GWASTools (or other programs)? Is it necessary to use the idat files (it seems it is not straightforward to use them in GWASTools)? It should be possible to write out txt files that include user selected columns of the the measured data in GenomeStudio (equal to the three tables that were already included). Can I work solely based on these files and which columns have to be included?
Thank you for your answers!