I am performing genotype imputation on Beagle v3.3.2 and when I include monomorphic markers in my markers file it doesn't run. For some reason it does not recognize monomorphic markers, because it has the same allele code for both alleles. Is there any flag I can add to my code that can make Beagle include the monomorphic markers into my analysis?
I've read the tutorial, but none of the flags present there seem to be helpful for this issue.
Hope someone can help me!