How would one associate a single phenotype factor (binary presence / absence of trait) to SNPs in Tassel (v5.2.58) GUI?
I generated VCF file using GATK and am able to import the VCF and phenotype data into Tassel. The phenotype data is just two columns the 'Taxa' and the 'Factor' (as Y and N; where Y = has the phenotype and N = does not).
The desired end result is a Manhattan plot with any SNPs associated with the trait, and ideally, an output file which contains the SNP locations.
For any other who come across, I have found out Tassel is not the best for this type of analysis (https://groups.google.com/g/tassel/search?q=qualitative).
However, if you set your trait to binary, where presence = 1 and absence = 0. You can the following analysis seems to work reasonably well:
>Relatedness Distance Matrix on the VCF
>MDS (PCA) on the Distance Matrix output
>merge your phenotype, VCF, and MDS_PCs using 'Intersect Join'
>run GLM on the intersected file
>generate Q-Q plot and Manhattan plot on the GLM_Stats association
I run binary/binomial phenotypes fairly often as you already figured out as 0 and 1s. But I use GAPIT which has much newer algorithms which I would highly recommend. GLM models generally aren't that good compared to the new ones. Feel free to message me
I recommend you to use GAPIT, which is much more easier and also its possible to do multiple model comaprision in same time.
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