Mutations droped out after running ABSOLUTE

We are using ABSOLUTE to analyze our WES data.

I . About 25% of mutations were dropped out after applying ABSOLUTE. They were just not in the output files. Have you seen this before? What could be the potential reasons?

II. After running ABSOLUTE, we divided mutations into 3 groups. Is that the right to group this way?
Clonal: Pr_somatic_clonal>0.5 AND Pr_subclonal <0.5
Subclonal: Pr_somatic_clonal<0.5 AND Pr_subclonal>0.5
Uncertain: Both Pr_somatic_clonal < 0.5 AND Pr_subclonal < 0.5