Hello Everyone,
I want to perform genome-wide association mapping for plant disease-resistant genes. As I am very new in GWAS, I have no clue to how to start or from where to start. I have my genotype data, phenotype data and a reference map and all are in excel sheet.Can anyone give me a head start on how to start with the GWAS? I want to do GWAS using GenABEL .But I am confused either should I use these three data file separately or should I make a single dataset out of those and use that? I want to perform QC too.Can I use excel files direct to GenABEL or at first I have to format it using PLINK?
Any comment or suggestion would be highly appreciated.
Hi Ishrat,
Is there any specific reason for choosing GenAbel & PLINK ?
Did you consider performing GWAS using Tassel or GAPIT or more recent FarmCPU?
Thanks
Raimonds Reščenko
Thank you very much for your recommendation.I am trying to follow the tutorial.
Muhammad Arifuzzaman Thank you very much for your response.Actually, I did this whole GWAS before using an automated pipeline namely Galaxy where I used GenABEL package .But as it has no public access(the version I used) and it was an automated pipeline,I didn´t had to do so much work.That´s why I am doing it by myself this time and in order to compare the results,I choose GenABEL.But I have other preferences too e.g. QTCAT,MLMM and GAPIT.If I can not do it with GenABEL ,I will try other packages.
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