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jiabowang / GAPIT

Genome Association Predict Integrate Tools
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Inputting phenotype with multiple replicates #91

Open cdetrana opened 11 months ago

cdetrana commented 11 months ago

Hi, I am interested in using BLINK to run GWAS. I have pure lines with phenotypic data from 6 replicates of trial screenings. After reading the documentation I am unsure in my scenario if I am limited to adding a single average value for each genotype's phenotype or if I can add all of the replicates separately using unique genotype IDs to indicate multiple phenotypic values are from the same pure line? Some lines showed more variance than others, if I input the data from each replicate separately, will the model account for the phenotypic variance when performing association tests?

Thank you in advance for any guidance.

jiabowang commented 10 months ago

Hey, If you set all replicates as different traits, the GAPIT will perform GWAS individually. If you want analysis the additive effect, you just need use average values or BLUP values.