Hi, i just imputed some SNPs using IMPUTE2, i pruned them and then kept all the haplotypes with probabilities higher than 90% (thresholding was done using Plink1.90)
but what i get is that some SNPs that do not pass the threshold are undefined with the symbol ./. (instead of the normal 0/0, 0/1 or 1/1)
I don't know if what i am doing is right and i need some advice on how to handle them because i would like to keep as much SNPs as possible and not removing samples.
I am new about imputation so any feedback is appreciated.