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Known Limitations of HAPPY 1.2 are:

• Only additive QTLs can be tested - we need to include tests for dominance and epistasis but the R version of happy now perfroms these tests
• Covariates cannot be included but the R version of happy now supports them
• Markers cannot be placed at the same position - doing so causes a crash
• Better data parsing is required to identify errors in the input data