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11.1 years ago
kumar.vinod81
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330
My results of GWAS from GAPIT and TASSEL are differing very much. My phenotypic data are quantitative. The problem might be that GAPIT convert all the missing values in heterozygote. I want to go on further for functional characterization of SNP but I am not sure with my results. my dataset also has missing values. Anyone here can help me in this regard. thanks
Exactly how much different are your results?
Both programs use slightly different algorithms so I'd assume that you get different p-values, but the ordering of associated SNPs should be similar...
Also, is your data already imputed (like described in that other thread) or did you use the raw data for both programs? Their results should become more similar once you use an imputed data-set as input for both GAPIT and TASSEL.
I've used raw data, not imputed. I am afraid with imputed results with my diploid plant species. After imputation its giving vary much different results, I've done imputation with fastPHASE, using command Fastphase –T10 –omyimputedresults fastphaseinputfile..... Is it right command or I need some other command for imputation. Thanks